The only thing in Harmony that doesn't necessarily still work for fully synthetic empires is leader lifespan.
And even that might still work if you have other non-assimilated species with leader rights.
This is consistent with what I've seen, also the -10% food is only really good for remaining meatbags.
and pop growth, unless you keep some meatbags around
Paradise Dome also loses some usefulness since the food is of questionable use at that point.
I don't think it would be out of line to have Harmony change after you ascend. Sure, it's not a huge deal but it would be a nice little improvement.
you can sell that food

but yes, paradise dome becomes a bit underwhelming after ascension too.
so it makes 3/6 effects losing their value which indeed prompts for a swap.
Yea we have a mixup with the new bonuses, the other 4 bonuses (not mentioned above) are:
-10% amenities used (replaces paradise dome, still useful for non-gestalt robots)
-50% time to swap strata (still useful for non-gestalt robots)
Defensive wars build speed and home territory advantage is unchanged, and still useful
+5% stability from the finisher (also, still useful for non-gestalt robots)
Final numbers aren't final, but that was what I recall from the dev diary.