If even little bits help, I think flac is friendlier to the CPU when decoding than APE… so while APE helps on the size side, flac would help on the cpu speed side (important for people with NAS)…
Lossless codecs are probably a matter of taste mostly 😀
You could just look at adjusting the transcoding scripts though, if you know the ape tools maybe you’re lucky and can provide an easy patch ^^