I would like to install a robotic port so that it does not take up space (in the same way as a substation is installed, perhaps with additional research)

The only issue with this would be how to get flying robots in/out of the building

No need. The idea is to add a drone station that doesn't take up space.
A simple solution would be to add a Roboport near the substation and change the construction and delivery area to cover the factory floor

I see your point, but i feel like the bots should be able to enter/exit the building if this would be implemented

After some thought this isn't really a thing this mod can add, it would have to be added by factorissimo2