Honestly, I would have to run a few tests to answer you that. But as far as I remember, they compiled all the animations using a configuration file where all the files that had to be compiled into one .gla where listed. So perhaps, as long as the first file, the root.xsi file, has the refpose the next files don't need it. This is just a guess. I know GLA Merge needs the first frame to be the base pose because that's how the program ASk made knows where to cut and paste (so to speak). Carcass certainly doesn't need it, since it only compiles data (it doesn't know if the frame 0 has the correct basepose or not). The .gla file needs the first frame to be the basepose and the .glm files must be created using the same basepose to match.