It's not a perfect fix though, after I added the bases to the ships list I tested it and the starbases were building starbases, so I had to go into the construct and add removals for all bases/stations for each race. So far so good though, only problems with the names now.
I may be thinking too far into things, but I did notice that only starships have a ship name list in the corresponding Racesd file.. I wonder if maybe a new name group should be created for starbase names, with a single entry (ex. "ControllingRace Starbase" or "ControllingRace Station"), that perhaps this might fix the issue of this persistent construct bug? For now I am happy with this workaround, so I will likely not involve myself further in this particular issue unless a game breaking issue arises from this workaround.
Additionally, on a separate note (as a note to myself), perhaps forcing shields to 100 and boosting the recharge rate for stations under construction could allow them to survive until construction is complete, whereupon recharge rates are restored to default.