cities on food bonus

Cities (at least in Crusade, I no longer play the base game) are population improvements, so they get benefit from population bonus tiles.  If you put a city on a +1 pop bonus tile, that city will support +1 more population that it otherwise would.

Actually, in my experience each level gives cities +10% population cap (applied to planet's overall cap), at least for carbon-based races. Silicon-based cities seem to get +0,5 flat cap/level.

Strictly speaking, each +1 bonus from a tile raises the improvement 1 level.  What one level means is dependent on what the improvement is and what code level of GC3 it is, since Frogboy tends to play with those a lot.  My +1 population cap for a city example was remembering it from what it was when it was introduced, you are correct as to what it means now.

I know the removed megopolis was a flat +1 to pop cap while the std city is +10%. That didn't make sense at all... but unless you plan on making a planet a farming community it no longer makes sense to use the +pop tiles for farming only. Farms improve by .1 per level now instead of +1 per level. Not sure if that will change again post 2.71

So far in the 2.72 opt-in it hasn't changed.