Do the guides on the ship base count as overlapping?

yes

Yes.

Since the simple answer is already gone I'll guess I'll add that those nubs are a big reason two parallel ships can't just jump the other. A small base is about a 1 move long but that move is almost never going to clear another small ship because the guides are counted and will get in the way causing an overlap and sending the ship back to its starting position.

The do NOT count when measuring for range however.

Thank you

What about the bomb tokens?

The guides on a bomb token count as part of the bomb for the purposes of measuring range and overlapping.

As mentioned with Bombs everything is going to count.

Thank you again.