The RJPEG is a compression which contains the thermal tiff images and radiometric information in a separate JPG file.
When you import a RJPEG into Pix4D, the software will extract the thermal TIF images automatically and save them into a folder called “converted”. These TIF images are the one used for producing the emittance map.
Basically, the RJPEG format contains two files, a TIF file and a JPG file. The TIF file contains the thermal information and the JPG contains RGB information (in case your camera is able to capture it) or some other color information which the manufacturer adds for visualization purposes.
In any case, Pix4D will be able to use the TIFF images, so if you are going to use only the thermal images, it is the same if you import TIFF or RJPEG.