So if say...I were to add Supports for the Amiibo characters...they would keep them regardless of who they were swapped with? That's pretty cool.
But I did try this out last night and had a pretty interesting issue. The randomizer swapped Orochi with Hinoka and things were fine for the first cutscene of the prologue with the exception of Hinoka's text boxes not switching her portraits or name to Orochi and then the game just...bombed. None of the changes were reflected after that including Hinoka who still appeared as normal despite being swapped seconds prior. After finishing the prologue and proceeding to the trial with Xander the game froze on me when starting the battle. I completed it without using Hans thinking the freeze might just have been my music mods but then the game froze upon Rinkah attacking me in the following mission.
I haven't tried removing my BCSTM mods yet but I'm not sure why they'd cause the game to freeze. You said other people had issues with this and Gay Fates, so hopefully this series of unfortunate events sheds some light on the issue.
Edit:
I'm very sorry, but I believe I've solved my freezing issue. It's possible that I randomized things incorrectly and my ignorance about how BCSTMs work likely lead to my game freezing. I wasn't aware each BCSTM had multiple files that included their battle variants. The game probably attempted to load certain songs that no longer existed causing it to lock up. As for your randomizer it's worth noting that I randomized the same game multiple time to attempt to get more favorable results. How exactly would this impact a rom? It may have caused my issues.
As a final question, are there any plans to force certain randomizations (say, forcing Marth over Ryoma but randomizing everything else)? I was randomizing my rom so many times in hopes of having the Amiibo characters replace the lords.