So I want to more my factory in to a single building so I did some quick maths, I need:
4 belts of copper ore,
4 iron
1 coal
1 stone
1 oil
1 water
2 output belts for rock parts.

Total 14

Would it be possible to have 2 inputs at the front of the building as well?

I will add larger factory buildings in the future, those will have completely symmetrical inputs and outputs. In the meantime, you could save some connections by sharing lanes, or by using fewer, faster belts, or by putting the rocket silo inside.

That would damage the roof. I think I have the programing(Ok... cut and paste skills) to add 2 more input/output lines to the factory my self.

Yeah, should be easy actually. Maybe put them at the sides or the back though, because the factory doesn't actually go all the way to the front of the hitbox and it would look weird.

Also the layout changes only apply to newly created factory interiors (and are permanent afterwards), so you could change the layout in control.lua, then place your main factory, then change the layout back. This way only one of your factories has extra inputs.

Out of curiosity, how difficult would it be to enable factory rotation (before first placement, obviously)? My main bus is S-N, so not being able to rotate the factory makes it a little inconvenient to use it as an "endcap" of sorts. Nothing that a little spaghetti can't handle, just a QoL kind of thing.

Right now I'm using roboports as the entity type for factories (no entity type is perfect for the job, but roboports are at least close), but roboport type entities are not rotatable, and changing the entity type in an update would delete all existing factories. Even if I could enable rotating factories, that would require updated sprites, and instead of spriting rotations of the factory, I could just sprite the higher tier factories instead.

It would be a lot harder than cut a pasting code. and even then you could not rotate ones that had been placed before. Best guess is you would need 5 items. an unplaced one that can be rotated and 4 ones for once it has been placed that you cant even if you pick it up. but I have no idea if that is even possible.