Yep, you're totally right. Without playing the boss, you're definitely going to be missing the final punch. I'm trying to tune it towards "a solid final challenge" but not "the place where your otherwise perfect build is now useless". Success in FTL always felt a bit luck-based and arbitrary (maybe because I never figured out the end game), so I'm definitely hoping to avoid that.
Yep, I think there's a respect to which this game will end up a little "here are your cards, now play them right" rather than "here are your cards, how do you want to play them", at least at high skill levels. I think I've made my peace with that; there's certainly no changes I can think of that will clearly disrupt that.
A prime influence for me is nethack, and I think my ideal curve is influenced by that, a challenging (but low investment) early game, that eases a little when death is scarier, but with sharp "do this right or die" moments punctuating the regularly. How close I can get to that remains to be seen.
Thanks a lot for the insightful commentary so far. Looking forward to your fuller account!