There's a problem with using characters (and ships?) that are already in use: any experience a character goes through will cause a character to develop - that development wouldn't be transferable to canon RP, though. What this means is that you end up with TWO characters - a "pure" version and a flux version for the flux thread she's in. That's a situation that might be hard for a player to manage - especially if you want to keep the flux version.
Furthermore, when firsts - like the first IC appearance of a fighter, for instance, are in the Flux forum, it deprives the actual RP of that first.
Basically, my view is that canon SARP should always come first - roleplay in plots and genreal RP if possible. Cluster Flux is for what isn't possible in the SARP.