I checked the same flags, "is available" and "has joined".
So far I've managed three runs of the game (two fully on Maddening, one on Hard up til timeskip, at which point I switched to Maddening) and only on the BE run have I had crashes when adding characters that are usually unavailable on that route for use in a general playthrough. Cyril, Seteth, Flayn and Catherine were the only ones that caused this, but as I'd said previously I have yet to find any real correlation between their crashes with the exception of they're locked out of the route entirely (bar Flayn until you get to the choice), and I had no issue just adding them or any other characters to my party on my BL and Church runs - I can't say for certain that it was just a general "will happen if you pick Black Eagles" problem, but the problems have only persisted when playing Black Eagles on my end when it comes to this issue.
Another note, I have had crashes when experimenting with characters early on with the editor when testing what will and wont cause crashes when editing characters and values (as I've talked about maybe 20 pages back), but those were across all saves and doing very specific things you'd probably not do during a playthrough, as well as being done on saves I'd made backups of and put aside.