Firefox doesn't choose the profile it runs with, no application can do that. The profiles are enforced by Apparmor and only Apparmor, if you want to change the profile used when Firefox is to be run, then you need to address the script to remove one profile and add another through Apparmor, which requires root privileges.
For gnome-open, yes, writing a separate profile for it would be better.
About Evolution or Totem, I'll see if I can rustle up profiles for them when I have time
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A note about Apparmor, it enforces profiles using paths, so if you linked a path to the firefox executable, then the profile that was made for the old path will most likely apply since the real path is still the same.
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