Will the other alien ships, such as the Xi'An scout, have their native alien U.I. glitch through in a similar manner to the Vanduul Scythe?

This will depend on the ship. The alien ship produced under license (such as the Xi'an Scout) will have a seamless human-designed interface. When the backstory is different and the ships are actually modified examples flown by other species (like the merchantman) you may see more touches like this!