I think the issues you're having might be related to rclone's crypt. I checked the output of 'git rev-parse HEAD' and I can confirm that my output is identical to yours.
I would also say that if your mods times are flat out wrong it shouldn't be a big deal so long as they don't change. I don't see how it would really affect Plex any differently so long as those mod times aren't being changed, right?
Honestly those recommendations come from the various places I've seen node-gdrive-fuse suggested around the internet, and while I haven't noticed a big difference in mount stability/performance when using those flags, I did notice a significant improvement in stability when I added garbage collection to the file.es6,js.
The other flags are just for efficiency sake. If I can coerce the mount into hogging less system memory and optimizing various file sizes then I figure I might as well keep it and hope for the best since it hasn't negatively impacted performance in any way.
Here's some archaic documentation on what those flags do too btw: link
As for node version, my main Plex server is using v7.5.0 while my backup/dl server is using 7.7.1, I can't say I've noticed much of a difference between the two honestly.