I am hunting other bugs than your issues, I have my own application to worry about :-)
I think it is a good thing that you can't retrofit to different category on the ship list based on other behavior.
You can mark all your space ports, and they will all retrofit to the newest design in their category.
Imagine, you got a powerful alien tech cruiser, and some wimpy cruisers that you can build yourself. The alien one is worth a lot to you. If you run the right automation you will be prompted "There is a new design, blah, blah, I suggest we upgrade our ships and bases for x credits". The stupid thing is to answer yes, because afterwards your fancy alien cruiser will be of your own crappy design.
However, you can safely go to the ship list, and retrofit all your space ports by one order (select all, press upgrade). They will each go to their newest design. Actually, you can safely do this across multiple categories (for instance escorts, frigates, destroyers, capital ships, space ports, defensive bases). Just make sure never to give the retrofit order to your fancy alien cruiser.
But as I said, if you have more than one type selected, you get no options on what to go to. Because if you select both a msp and a lsp, they head for two different designs.
I imagine that if it was easy to flip categories from the bases list, you could soon enough discover that all your mighty battle fleets have been turned into swarms of escorts. It is a disaster waiting to happen.