So my initial plan was to integrate defences into the castle chain, i.e. t3 castle would have matchlock, t5 batteries, etc. This didn't work, as the effects assigned to defence buildings (e.g. bos_siege_defence_matchlock) do nothing, as in they have no effect on whether improved defences show up in sieges. They're probably there for the tooltip only. Then I tried the reverse, integrating the castle modifiers into the defence chain. This provided more interesting results. It seems that in generating the battle map for sieges, the game looks for
1)The level of the building assigned to the castle slot
2)Whether there is a building from the defence chain, if there is, the level of the building

Thus when I made the castle chain like Stronghold(lvl 0)-Fortress-Matchlock (lvl 2)-Gatling-Batteries(lvl 4), upgrading to Matchlock Towers actually caused Gun Batteries to be used in the sieges. On the other hand, if I kept the default leveling of the defence chain and made Matchlock Towers lvl 0, this would cause siege maps to be generated from lvl 0 castle template. I'm not aware of any ways to influence this as the function to create siege maps isn't exposed to us, so I don't think there is a way to integrate castle and defence chains. I found that Daniu (very competent modder) tried this and gave up on a decade old thread on TWC, so yeah if they couldn't do it, it probably isn't possible.

Now to my solution: Simply giving a Matchlock Tower to every province caused a problem. Since MT occupied a construction slot that wasn't available, this prevented the first town upgrade from providing a new slot. As a workaround, I also gave every province a level 2 town (large town). This restores the normal slot behavior, until the last tier where we reach the slot limit. I tried to increase the slot limit in campaign_map_settlements and campaign_map_settlements_templates, had no luck, possibly hardcoded. I think the developer of Master of Strategy has a way to increase slots, but I'm not sure whether it'll work in this case, it may create some new problems (with the UI and the AI) so it seems like too much work for too little benefit. I also thought about creating the defence slot outside the city, like farms/specialties but afaik increasing the number of specialty buildings causes crashes and you have to place on on the campaign map. Even if I managed to do that, it seems very likely that the defences wouldn't be visible in sieges as they're positioned outside the city.

I already wasted too much time on this, testing TW is so damn time consuming. And what's the point, the player will almost always attack with artillery and destroy the towers, and defending against AI is already too easy, helping the player at the expense of AI goes against all my modding attempts. On a good note, the AI seems to prioritize destroying towers when laying siege, if they have artillery that is. That's one of the reasons why I recommend people to use FotS Enhanced and not this, since the AI is much more likely to recruit artillery units in Enhanced. Rant end