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As for the Y, Z thing, most importers and exporters give you options to set the up axis, be it Y up, Z or -Z forward or Z up, -Y forward. You just have to set the options to import the model to the Up Axis you want it to be. The rotations of a model all depend on how the original author of the model exported it and and what the up axis is for the game engine or purpose it was developed for. So, this is not a Blender thing other than the Blender default being Z Up and -Y Forward and the other popular 3D editors being Y up and Z forward.
This will always be a problem, but manageable, You just have to remember that 7 on the pad is front instead of Top View, and 1 is Top view instead of Front view.
If you haven't seen SMD imported into Blender then have you even used Blender Source Tools?
And no this has nothing to do with X Y Z of the model, its the bone orientations, Blender Source Tools doesn't flip their axis, leaving us with a mess of tiny rotated bones.
This is a problem to do with Blenders Bone Axis, so the addon NEEDs to support bone axis flipping so we can have normal bones...
https://imgur.com/a/l1Cryvv
If you want to just make a tweak to a model and then use it with the same animations as before, a very common use case, then the bones need to round-trip correctly.
Creating Blender bones isn't just a matter of rotating things, either. Bones do not actually have a rotation, but a head and a tail location. And that head points up to the parent bone. It's frequently impossible to generate a good result programatically because the script doesn't know where to put the other end of the bone.
Properly converting skeletons to Blender's wacky skeleton format is destructive and for that reason will never be done by the Source Tools. You are free to write a second script that does the work, but it won't be easy.
However there are some addons that can import skeletons "correctly".
REDxEYE's SourceIO has an option to "Normalize bones", which results in this: https://files.catbox.moe/89jw2r.png
Which actually looks pretty nice and is great to work with, except like Artfunkel said, it breaks existing animations, so personally it's usless for me to rig things to an existing skeleton. Additionally, the tips of bone chains dont have their proper rotations, (probably because it doesnt know where to put the tip of the bone), as seen here: https://files.catbox.moe/psr6q0.png
Very frustrating.
Maybe one day, through collaboration or something we'll be able to have proper imported Source skeletons in Blender. Until then we're going to have to deal with manually weight painting everything.
I use a rigging skeleton which is just a normal skeleton renamed to Valve bones, I use it to auto weight with.
And then I use a script to rename the entire skeleton to something symmetrical with .R and .L
Do the weight painting n such.
Then swap the skeleton back to the sphere bones skeleton.
Auto rename them back.
Sure, I'll package them