Well, in my opinion LVM management is one of the absolute basic skills that everybody who is allowed to log in as root on a server should have1 - Complexity of administration
If you need to "recover data" when one disk fails then you have a serious problem with your setup A disk failure should never have any impact on your data. Proper RAID setup is the key here.2 - Harder to recover data if a disk fail
Any hard facts? LVM performance impact is negligible (unless you're using LVM snapshots)3 - Efficiency drop
Downtime? There is no downtime with LVM operations (resize etc.). Au contraire, you have less downtime with LVM as it abstracts and encapsulates the underlying physical hard disks and you can add disks/partitions/volume groups online. I never experience one single minute of downtime because of LVM.4 - Downtime (or minimum but is there)
BTW: A good read about LVM: Logical Volume Manager (LVM) versus standard partitioning in Linux
Regarding your setup with HDD + SSD + NVMe: True, Plesk can't handle this. You may want to create a feature request at Feature Suggestions: Top (2051 ideas) – Your Ideas for Plesk for this. But I think this is a very specific feature that not many people will use, so I fear chances are slim that this is ever going to be implemented.
I would rather create 3 VMs on 3 different storages and then let your customers pick their desired storage speed, like "Bronze" (HDD), "Silver" (SSD), "Gold" (NVMe), each with different pricing