Currently you have to put a belt outside to make the connection, but if you end an underground belt right outside, it won't make a connection (so you have to end the underground belt 1 tile early and stick a belt in front of it).

It'd be nice to be able to end an underground belt right against the factory and have it create a belt of the appropriate kind on the other side.

I would also like it if mod-added pipes, like from flowcontrol, would work as well.

All mod-added pipe or underground pipe entities will connect, however Flow Control's custom pipes are actually storage tank entities behind the scenes, so they won't connect like regular pipes do.

Any technical reason storage tanks don't connect? Or for that matter, any reasons you as the designer wouldn't want them to? I'm not really sure it matters, I'm just curious.

Also... what about pumps?

Storage tanks don't connect simply because vanilla storage tanks don't fit nicely into the inside ports. I could add exceptions for the Flow Control pipes though.