If I understand correctly (the Linux Guest reports about 97 GB less usage than the space used on the Host by the grow-able .vmdk files), It might be the case where your .vmdk files are accumulating a fair amount of detritus that was once used, but is now un-allocated in the Guest.
In my experience with Linux Guests on a Windows 10 Host (using Guest EXT4 formatted virtual drives), I needed to zero out the unused space before trying to shrink/compact the .vmdk files in order for it to actually free up the space.
Otherwise it appeared as though it wasn't recognized as unused.
It's been a long time since I last did this, but it went something like:
*) In Linux Guest
dd if=/dev/zero of=wipefile bs=1024x1024; rm wipefile
This fills all available unused storage space (on the current partition) with bytes of 'zeros'. It did not expand the Host .vmdk size to any noticeable amount.
This can take a while and you don't want the guest to be doing anything at the time.
I think this needed to be done with the VM not having any snapshots.
*) From Host Windows command line run the Shrink/Compact command while the Guest was shut down:
vmware-vdiskmanager.exe -k "<path to vmdk>"
I'm not sure if it's your issue, but good luck. Make sure you have a backup in case things go wrong.
Also, if you are low on free space it might become an issue trying to shrink the .vmdk (But if your prior attempt worked I guess that's a good sign).
