Some mods allow it, others don't. Those that do, you need to be careful which bases you choose to dock with- because you will often appear in the hangar just like you would if flying a fighter or freighter. Sometimes, you can get yourself stuck pretty good.

You would need to make sure they use moors, med or large and the bases have that ability.

The Hunters Mk II MOD has capital ships and uses moors for docking, but I still have bays for launching. I have not had a problem with that arrangement yet.

The only problems I have had is not all the moor points on all stations have been modified to allow docking and the docking control AI sometime sends a player to a stock point. The player just has to F1 out and move so that the AI will select another moor point. Repeat until they get the right one. If I changed it all the AI Trains and Transports would vanish when they docked with a station.