2. Coming soon. The idea of learning via "the internet" isnt something I'd considered, since we really have no indication of if or when a colony "connects" to any wider network on the planet or solar system. IIRC, lore wise, there is no indication of the far reaching rimworlds being able to communicate with the core systems, so I don't know if there exists a concept of a local internet or other shared knowledge resource.
Considering the empire seems to only have a fleeting presence on the Rimworld and tends to be more of a "Trade knowledge" faction rather than a "share knowledge" faction, I'd suspect that even if there was some kind of shareable resource, it'd probably not be free or easily accessible.

It's an interesting thought for future development, though. What is coming, is textbooks and skill trainers. So there will be options, for a price.

3 and 4. Starting proficiencies are determined 100% by the pawn's backstories. Proficiencies are added from childhood and adult backstories, and those proficiencies are hand assigned. It's very likely that in the 2-3k backstories I've filled out, that I haven't been entirely consistent, but that same backstories will always generate the same collection of proficiencies.
There will likely be a future change to how these are created, but I'd suspect it's a very long ways off.

Side note: Character editor may as well be a black box, so I can't say anything as to how it is generating pawns, and I can't provide any support for pawns generated using character editor. I will say that I use it when I do my play testing, but since the source code is both close source and obfuscated, there isn't any way for me to troubleshoot any pawn generation issues with proficiencies when it is in use. Additionally, proficiencies are assigned when a pawn initializes. In vanilla, I believe this happens when they are generated in the pawn selection page. I cannot say whether changing the backstory in character editor will re-trigger our own initialization. Fairly certain that it wouldn't actually change the proficiencies even if it did retrigger initialization.

All that to say, the experiment you did probably wasn't sufficient to test proficiency generation with Character Editor, and there isn't really a good way to test for certain either.

Thanks for the feedback. We will have a major release soon-ish, so hopefully there'll be more to discuss after that.

Thanks for the in depth response! Some other thoughts:

1. I love the Rimworld lore as a setting. It can be vague and abstract sometimes, but the aesthetic is super cool. I'd agree that there seems to be little to no sharing of information across systems (like the example you gave of fallen empires). And I believe FTL doesn't exist at all, which is why space travel takes so long and logistics are so hard. But some kind of planetary-based Internets like on our own world might make sense. They'd probably be planet dependent, and likely any high tech faction would maintain their own servers. Some planets might have public networks, but since Rimworlds are often militarily contested I'd imagine they'd be more limited and harder to access.

Maybe include some kind of digital option in addition to physical text books? Data storage, devices, etc. could all help with learning information that wouldn't require a planetary internet.

2. That's a lot of backstories! Yeah I'd imagine perfect consistency is out of the question. The one I was referring to in my example is the exiled researcher, which starts with a whopping intellectual +8. It reads 'was exiled by their technophobic government for their interest in robotics'. Given that the year is 5500 and the spacer age began around 2100, that's a huge amount of history. A lot of that involves travel and planets developing independently, but there's definitely been interaction between planets and tech advancing. So technophobic could mean the year 3,000+ for tech, but that government put limits on robotics research (independent AIs, androids, etc.) Any backstories that involve spacer age+ tech I'd expect to have a lot more science profs.

3. A simple fail safe/ blanket prof system could give out certain science profs based the intellectual bonus of the adult backstory. This would provide some support for modded backstories as well, and you wouldn't have to worry about overlooking any vanilla backstories.

You'd probably want to consider the highest +intellectual bonuses from tribal backstories, and then could compare those to modern era, spacer era, etc. bonuses. Without looking, I don't think there's any neolithic backstories that grant like a +8 intellectual? Even like a +5 is pretty high, and usually those backstories would have required science knowledge and life experience.

Anyhow, I'm really looking forward to seeing how this mod develops. :)

More "scifi" learning methods are definitely under consideration. I've imagined something like learning pods where someone essentially has their brains rewired to just "know" what they're being taught.
There are a number of other features that take priority though, so I'd suspect that's a ways off. I do think there needs to be a consistency pass, and maybe a few modifications to what proficiencies are available. Maaaybe a bit more granularity so we can have pre-industrial backstories that are assigned some actual science proficiencies, with the higher level proficiencies essentially representing what a professional scientist would know.
Trick is, I don't want to expand the "useless proficiencies" category, so I need to be sure that each of them actually has something that they can gate.

I've played some more and had a look after the update and things look really good. Features like pioneering are good that they exist in some form. A few more thoughts post-update:

1. It's great to see so many patches and improved compatibility. I still think some sort of blanket system might be helpful as a fail safe/ for missed compatibility. Maybe if the backstory isn't listed, instead of starting with no profs it could also assign some basic ones based on +skill bonuses from the background? Like an adult backstory that gives intellectual +5 or higher could give through advanced science or something.

2. Regarding the intellectual stat, I think it could make sense if pawns with a high stat got some bonuses compared to other colonists. If you hover over skills, rank 10 is considered a skilled professional, whereas rank 14 is a master. With vanilla skill decay, you don't tend to see skills above 18 (in my experience) unless they're constantly gaining xp.

Maybe some sort of bonus to prof learning or bonus random starting profs on newly spawned pawns? Like some sort of scaled bonus at rank 10+?

3. Adding to that, a high cooking, medical, construction/crafting, etc. skills could offer scaled bonuses to the corresponding profs (cooking, first aid, etc.). Maybe starting with the tier 1 prof if the pawn wouldn't already.

Anyhow, the update looks great. I really love the bookshelves added and I'm excited to see how this mod develops in the future.

Edit: Another minor thing. I know you don't want empty profs, but some groups are a bit awkward. Construction is needed for electrical things (stove, comms console, etc.) and non-electrical (column, billiards table, throne, etc.) Maybe those could be in two separate categories? Or move some to basic mathematics which is required for construction? Or even the non-electrical could not require any prof to build? I feel like there's a pretty big difference, and can be very inconvenient in early colonies if your builder didn't get that prof.