on the long term, yes. software lists might cover these things more easily (even if keeping this trick for non-softlist loading cannot harm, as long as the source documents why is there)
otoh, on the short term, there is still a lot of work to be done on software lists before they can be considered the suggested way to load games in MESS: we lack mirroring of rom for games which use it, we lack a standard way to handle per-game sram, etc.
as a result (and because pegasus emulation is in progress), this 'ugly' solution is imho perfectly fine at this stage.
btw, thanks Robbbert for getting in touch with the Pegasus guy at Mbee boards. I don't know when/how this system would have been otherwise preserved