"The Fuji X100t disables the flash when bracketing is enabled. This seems logical for things like ISO bracketing because several photo's are taken in quick succession. ... an oversight in the firmware?"
1: They don't want to put in a fast flash to keep up with the frame rate or risk shot-to-shot inconsistencies.
2: Probably, but there's a workaround.
Shoot RAW, and apply the film simulations after you’ve shot.
To do this, view a photo, then press Menu/OK. Go to Raw Conversion, Film Simulation, and choose the one you want to apply. Press Menu/OK, then press the Q button to tell the camera to create the new image. Press OK to save it.
If the RAW is already on your computer:
If you have existing .raf raw files, you can copy them back to a memory card (just put the files in DCM > 101_FUJI), and load that card in your camera, then perform the conversions as explained above.
Source: "Use Fujifilm Film Simulations In Camera, and on Existing Raw Files" by Kirk McElhearn.