We played Star Fluxx, Star Munchkin, Dixit, and, of course, Bomb Alley.
See CLARIFICATIONS in the aforementioned document:
7.5 Placing Control Markers in the Tyche Card Phase: Sea paths can be used to place control markers in the Tyche card segment. Trans-Mediterranean paths may not be used to place control markers.
Example on page 5: The starburst faction can place a control marker via sea routes. So the black “N” on the Arados space should be a white Y.
As to Independent markers, there was some discussion over it at CSWF some time ago. Rule 7.5 says:
The 2 MP path may not “jump over” a space containing enemy CUs, Independent Armies, or enemy control markers.
Rob Seulowitz who's one of the game' playtesters and I believe a sort of authority clarified here (http://talk.consimworld.com/WebX?14@318.Oy4kahWZlqv.7@.1dd17...) that
Independent Cities = "Enemy control markers" to all players.
So you can't jump over that space in order to place your marker.