Xenon Wharf uses the exact same S/M building module as the Commonwealth.
They just float slightly above the floor.
As someone who's been living with the Xenon for quite some time, I've seen them both launch from AND dock at launch tubes.
Xenon use a variant that allows ships to use them to dock.
Which, the AI scripts don't have a way to distinguish launch tubes from landing pads other than the "fact" that you can't land at launch tubes, so these Xenon variant launch tubes don't count as launch tubes to the game's logic.
In any case, M size ships use access ramps, so the bottom of the ship doesn't even have to be very close to the floor.
Have the landing gears extend further to put the ship's main hull up a higher, give the access ramps extra length through retractable parts or maybe just have them at a steeper angle so they can cover the extra height, and you'd even have enough space for turrets below the Terran Katana that's currently almost flush with the floor.
It's just Egosoft's design decision to have them this way.