...balance will ALWAYS be more important to historical realism in this mod: it always has been. I find that to be the biggest point when people make the CK2+ vs HIP argument on the internet.
It really depends on the specifics of implementation. Once could certainly argue that chess was a very well balanced medieval-themed strategy game, but I doubt many people would feel turning the game into chess would be enriching to the medieval sandbox offered by CK2/+ (of course this is an extreme used illustrate a point rather than something likely to happen). On the other hand, the better factions systems offered by the mod made it far more balanced than CK2 vanilla, while also making the game both feel more realistic and play out in more realistic ways than every faction being a coup or an independence revolt.
To get to the real point of the issue; if the new building system, however it turns out, isn't fun to use, that's going to matter more than whether it's balanced. Of course what one person considers fun is different from what another does, and balance can factor into that quite strongly in the case of some people, while others can prefer things to be less balanced.
For me personally, I like it when the game offers me the opportunity to make a realm which is in every way richer (financially, technologically, culturally, etc.) and more prosperous than my rivals. That means I want an economic system which lets me make some places considerably better than others; Building New Romes, Alexandrias and Constantinoples, turning the Irish sea into the next Mediterranean or building a better Venice in Crimea. And importantly, an economic system which
doesn't let me build them up like that over-night but rather through sustained economic consolidation and investments over many decades and centuries of play.
So when I hear that you only get 12 buildings of 20 max per holding, with slots unlocked through techs, the main thing I worry is that it's going to be something you just do every time you tech up; > tech up. > build two more buildings > wait for next tech up. Now to be clear I haven't had a chance to try out the new building system yet (I'm working on a submod and I'd rather get all the systems working on one version, then port it to then release version than update to each beta version and split my time between finishing the stuff in the mod and making sure nothing gets borken in the transition between betas), so I haven't had a chance to play with the current building system.
Based on what I've heard though (and a cursory read of the code from the current beta), I'd probably prefer it if the total number of buildings allowed in holdings in a province was based on several aspects, not just tech. Possibly prosperity? So if you have 6 buildings from tech+base, and Lvl 3 prosperity, you could build up to 9 buildings. If prosperity went down to -3 because of the black death, you wouldn't lose buildings, but holdings with 3 or more buildings wouldn't be able to build new ones until the place recovered.
Also from glancing through the code, a lot of the castle buildings look fairly flat? (not sure if that's the best way to phrase it, but I can't think of a better way). Like, mechanically there's no difference between an escape tunnel and a judgement hall, for example (in the building file at least). All the costs and effects of all the buildings I've seen seem pretty similar.. I dunno. Are you planning on doing a load more stuff with it? Because at the moment I'm not sure I'm sold on the idea of updating from the older beta version I'm currently running? But that kinda brings this whole ramble back full circle. If the new system is balanced, but it's not fun, people aren't going to want to use it.