99.9% of my use for Parallels Desktop is to run Vagrant-configured development environments. For these VM's, Time Machine backups make zero sense. It would be nice if there was a way set the "Do not backup with Time Machine" flag via the prlctl command (which I would then utilise via .customize[] in Vagrantfiles)
Unfortunately there is no API to control Time Machine, so we can't do it. One of the ideas for you to consider: Add a folder to TM Exclude list manually and then put all VMs to this folder.