Right now the mod has quite a performance impact on the game if many factory buildings are in use. I understand it, that the usage of multiple electric networks are the main cause for this. Wouldn't it be possible to combine all the factory interiors to a single surface and connect their power grids to circumvent this problem?

I think that the biggest problem is in linking the entrance of the factory building interior to the "external world".

If they were all on the same layer, it seems that might become impossible.

That would work just fine. I'm hesitant to link the power grids of the factory buildings because a) that would make power transfer completely unrealistic, with factory buildings requiring no physical electric connection to power each other, b) create feedback loops when some factory buildings are set to input and others to output, and c) make power switches useless.

You might be able to move all of the factories that exist inside of a factory to the same surface, as those wouldn't ever be affected by power connectivity issues like this. That naturally creates a lot of issues with how these buildings work, so you'd have to engineer some code that basically cheats at creating this situation in order to keep the game running fast, but it seems less-than-impossible.