I will not address the specifics of the "science," as I have no education in such things. However, as a (would-be) writer, I have a few comments.

1. The thing does not appear to "fly" through space - it teleports.

2. If it teleports, why do you need a ship? Just build a colony on Earth (or where ever), then activate the central power supply and teleport the colony to Mars (or where ever).

3. Use shuttles (or what ever) to build science stations in orbit (for zero-g considerations in construction), then teleport the station to where ever you want to establish a long-term observation post.

4. As far as "replacement material," the local stuff would (normally) fill in the void, but you might want to toy with the idea of the "displaced stuff" at the destination somehow being teleported backwards to fill in the void. At least *that* would explain why you would want to use a ship in space rather than teleport directly from a habitable surface.