I would rather stick to one lossless format which is FLAC because there really isn't much problems with it and it is definitely future proof.
I know that having a single file with a CUE Sheet that defines when a specific track starts prevents any gaps so it can be identical to the CD release, but who says it can't be done with tracks split?
I admit i never used Medieval CUE Splitter, but i'm pretty sure it does re-encode when splitting, at least if we are talking about FLAC [because] if you want to split FLAC without re-encoding, you will either have to move track boundary to the nearest frame boundary, or produce non-subset file where the first frame's length is less than that of the following frames.
I have ripped a CD album to APE to a single file + CUE sheet. I just have to ask btw why is this method good? Why do people want a single file rip instead of having it be divided into individual tracks?