I couldn't get the custom ship set concept to work for me.  I consider it a combination of my ineptitude and Stardock's unnecessary complication of the issue.  But that isn't what I am talking about.

A wonderful nice person on the forum took my jumble of files and designs and made a working ship set out of it.  Yay!  Now I see my crazy ship designs flying about the galaxy!, That is not what I am talking about.

I am trying to play MP, and even though I turn off mods, the ships set breaks my MP.  To my understanding, the issue is the changes made to the game folder "Designs".  These changes enable the displayed example in the ship style list and the modification of the starting ships into your ship style.  It causes a de-sync immediately on beginning the first turn. It is a repeatable hard failure.

It makes sense, after the fact, but it caught me by surprise. I felt that disabling modding was enough to get back to MP mode. Should have known better, I guess. I now maintain two folders, one with all the original Stardock files, and another with modded files.  So that is my individual workaround. It seems to work barring standard MP issues  I am hoping that promised support for ship set will relieve the need for all this fuss.  In the meantime, I thought I would give people a head's up in case it would blind side them like it did me.