I would agree with other posters when they say that the question of what happens when a player with the FPS expansion attempts to board a player ship without the expansion. It's difficult to speculate as we have no idea how such a mechanic will work.
However, it seems to me that the most elegant solution from the 'border' point of view is that when you try to do this, you actually find yourself instanced off and boarding an NPC copy of the ship, with the same cargo, loadpout etc. but an NPC crew.
The question of what happens to the 'boardee' is more tricky, but could be straightforward depending on how the boarding mechanic works. For example, it could be that a ship needs to be disabled in some way before boarding. In which case, from the boardee's point of view, when you are disabled you are simply destroyed instead (and from that point on the boarder sees an NPC copy).