It does get confusing, but you can load a "PF for all races" shiplist in Shipedit, I do it all the time. The trick is, whichever race you use for the PF donor race (I usually use Gorn), you have to move that race to the top/first entries in the shiplist, and that you have to do in a spreadsheet like Excel. Once youve done that move, shipedit will load it just fine. The duplicated ship will have a "Race" entry ("Gorn") of it's donating race but the "Class Name" ("F-PFT") will allow it to show up in the (Federation) shipyard. You do need to keep track of duplicate entries (because that can cause CTD sometimes) and that's easier to do in Excel (copy-paste a line or two).
I'm not sure how Rod's Mod worked or what is meant by "captured mode"; I must have learned this trick someplace, maybe from him. My personal shiplist has the Neutral race first (to give fighters to a PF race like Roms) and then the Gorns (to give PFs to fighter races like Feds), and then all the other races.
Let me know if this idea needs clarification. Like I said, I've been playin OP using this method for years with no problem.