From the settings:
"Surface Limit
Maximum number of surfaces Factorrisimo2 should create for factory interiors. If you have more factory buildings than this number, Factorrisimo2 will start reusing previous surfaces."
Does that mean that a second factory will open a door to a previous surface? Or that it will regenerate a new factory with an old name? ie, would a factory mk1 turn into a factory mk3? Or would my 101th factory give me access to my first mk1?

Your 101st factory will be placed in the same void surface as the 1st factory, but offset by 512 tiles. This will not affect gameplay unless any mod gives you the ability to travel across the void.