If mechs do become more integrated into the starbase community then ships would be designed for carrying mechs or they could be used to steal cargo with more efficiency
And if you can't do that, you can always just use a resource bridge to transfer over any small cargo once you have access to the controls. Using a cargo lock frame for anything too big, cargo lock beams would still work too.
Mechs are really cool for science fiction, but they are just impractical if you actually try to find a way to use them.