Bonuses don't apply to allies, no. And fussy province-swapping is still key for exploiting your allies cheaper buildings or more interesting forts. NG supports different fort types, so if you want walled cities but you're only allowed pallisades, your allies may be able to help...
And the beauty of NG is that you don't need to upload the mod, just the seed and your settings - to include restrictions used, if any - and everyone else can generate their own copy. Once you have all the nations picked, you can regen a smaller mod with just those national seeds specified for the sake of brevity.
I'd recommend doing some sort of ordered draft to pick both normal and NG nations (and I'd also recommend more than 20 - I usually did 100 with NG games in the past; if that's too big of a search space, I'd say go with number of teams x10) to create a less admin-biased setup. But I'd also make sure you had a fixed player list before you jump into generation, especially if that will impact how big the nation search space ends up being. You can re-use that same seed/settings combo with a larger number of nations if you really are enamored with the idea of being/fighting (
) one of those nations you already generated...
However, it's not my game, nor do I want to get entangled in it.
If first-come-first-served is what everyone wants, my fussy love of order, symmetry. and structure need not be considered.