Yes, the buttons have been working fine with jstest. After a few hours of hopeless resetting and deleting button configuration files, I tried a different port. Problem solved!

I still can't explain why a different port would let L & R work on ES while the actual inputs were detectable...

Now my only issue are phantom inputs, as discussed here: https://retropie.org.uk/forum/topic/8598/buffalo-controllers-phantom-inputs