While the Switch version is about the same size as the 360/PC version, that doesn't mean the files are the same. The PS3 version of PTDE is ~ 5 GB. The difference comes from the intro/ending movies and container size. PS3's container sits at ~ 3.41 GB while PC is 3.24 GB. The movies on the other hand difference is huge. PC is at ~ 387 MB while PS3's come in at 1.55 GB.
The bigger point about the file size is that 3.9GB (the size of the Switch version) can't actually fit on a 4GB card, meaning it's on an 8GB card and has at least 3 more GB of room to spare. Which means there is plenty of room for higher quality audio if that was indeed the issue.