FUSE?

It's not a "problem", it's a useful new filesystem feature, which, like most filesystem features, has multiple potential use cases. It's no more "package management" or a "docker problem" than overlayfs is a "live CD problem".

I can easily see you in the 1960s complaining that nobody needs these newfangled "file" thingies and the need for them over proper hardwired partitions laid out at disk format time is a problem with these newfangled programs that want such ridiculous fripperies.