The 3-in-1 does not deal with any files itself, that is handled by the software that is controlling it: GBALdr, the 3in1 Expasion Pack Tool, or the EZ-V kernel.
VBA will open saves from the 3in1 Expansion Pack Tool, and vice versa. I haven't tested with GBALdr, and I don't have an EZ-V to test with.