1) I am running low polly 3d modules through a method that spawns STMP assets on the edges of each tri, 2) so object pooling will be something I look into. 3) It will be groups of meshes yes(so like all plants are using one specific mesh, all rocks, all buildings, ect). 4) I have also ran into issues with Unitys dislike/lack of support of good coding practices. Though what I have been doing is using MonoBehavior's for purely the editor logic, or using them to wrap one to one class instances of my behaviors. Allowing for partials in the wrapped class, is a has a.
I am also trying to build out the exe as I see a good portion of the Update function has editor specific code(not sure this is the issue, but might alleviate it enough), but am running into other issues from another plugin so will get back with the results. Also my condolences if you have been waterfalling a 5k line file lol. Partials and Single Responsibility is the only thing keeping my sanity as a programmer intact, though often find others pushing projects through without consideration of future maintainers(from lack of budget or bad timelines of course, no fault to the programmers who make actual functioning code).