I hear what you say and understand why you don’t auto-delete the JPGs by default but I’m still inclined to save resources on the server. You could add a delete option in the “extra features” section (unselected by default and with appropriate warnings).
My host caps both disk space and inodes (effectively number of files). WordPress is problematic anyway because it makes copies of each image in multiple dimensions, storing duplicates of all my JPGs as WebP gobbles yet more resources.
The conversion operation (at 75%) worked well in that it didn’t take long and the new files were close to half the size of the originals. Google speed test went from 94% to 98% The problem is that I’m now using near 50% more storage because I have images in both JPG and WebP formats.
If I were to download a copy of the /uploads/ folder to my PC (and a keep a backup!) then in the scenario you identify, the plugin being removed, I could copy the uploads folder back.
Mine is a “hobby” site, I guess if it were commercial I may be more cautious. If I were building from scratch now I’d upload images as WebP anyway as recent versions of Chrome, Safari, Firefox, Edge, and Opera all handle WebP and I don’t think it essential to cater for the laggards.
As for AVIF, my understanding is that it’s a little less widely supported and doesn’t make files much smaller than WebP (although quality is better so you can turn up the compression without losing quality) so, at least for my hobby site WebP can save me a load of disk – if I delete the jpgs.