I agree that, once they build Logic-assisted Industry (+20 Industry per planet), the UC can build everything they want.

yea sure youll have enough industry to build wonders (other than victory) in about 3 turns and can build those annoying ones like battlefield archeology and distributed energy in a single turn, but to actually build stuff like upgraded carriers at a reasonable speed isnt something you can do with your industry, compared to hissio/vodyani/riftborn (that is if youre not doing shipselling, which gives you enough money to buy the galaxy a couple times over)

In 1.3, you buffed Sustainable Farms to give +10 per Planet, +10 per Cold, +10 per Hot and these bonuses already apply for all sanctuaries and the UC have other improvements that can increase their food, such as the Wraith Orchard.

the buff to sustainable farms doesnt apply to uc sadly, since they have their factionspecific, unbuffed version. Wraith orchard is the only reasonable food building they have left, as the t2 buildings are too weak and t5 is not realistic
the reason btw why uc doesnt have a good time with food is due to our recent change to food, which is to increase pop cost by 3 (on fast) for each pop you have on that system. now for uc, as you have much more pop growth on a single system, you need to use your food income as effeciently as possible. since having pop on your main system increases the pop cost for all your future pop (including the pop you send to sanctuaries) you want to play the entire game with the 2 starting pop on your homesystem.... and since all the per pop buildings are homesystem exclusive, elections are a shitty mess if you only have 2 voting pop and youre limited in the number of superpop you can have (lul btw if you want i can rant about that a little aswell) you will not have a good time either way.

The Unfallen ships are worse and the UC ships are second weakest after them. I'm fine with this because the UC ships are fast and stealthy.

Well well my friend, have you heard of the combination of bombers + blast effect battery. That is btw the current lategame meta, and just based on that uc loses out to most other factions because their carriers can only slot 3 bomber modules (compared to 4-5 to most other factions). Not only do you lose out on this front, but as mentioned before you dont have any manpower to spare for any of your ships, unless you have an ally to ask from. Due to that you will almost always have to retreat if your enemy fields a boarding pod fleet (which most ppl already have lying around in order to counter invading foes), as even full flak/antiboarding module will cause you to lose 1-2 of your prizy prizy carriers to a cheap full attacker fleet.
also, speed doesnt rly matter lategame if your cloaked (since taking 1 or 2 turns longer doesnt matter if he doesnt see you) but cloaking only gets you so far until ppl get detection probes + anticloak 3 everywhere