GNU version of locate - gupdatedb fails with "gfind: failed to read file names from file system"
The problem here is that you are running GNU's updatedb with the macOS's find. gupdatedb is a shell script that expects to be running a GNU-compatible find. In particular, it converts --prunepaths to a GNU-compatible basic regular expression.
--prunepaths='/private/tmp /private/var/folders /private/var/tmp */Backups.backupdb /Volumes /System'

converts to
PRUNEREGEX=&quot;\(^/private/tmp$\)\|\(^/private/var/folders$\)\|\(^/private/var/tmp$\)\|\(^*/Backups.backupdb$\)\|\(^/System$\)\|\(^/Volumes$\)&quot;

GNU BRE (basic regular expressions) treat \| as an &quot;alternative&quot; operator:

‘foo\|bar’ matches either ‘foo’ or ‘bar’

This is a GNU extension to the BRE syntax, and the macOS find operator does not accept it. So the whole prune string fails to match anything.
The macOS (and POSIX) BRE does not have an alternative operator, so it is not a super easy fix. The macOS updatedb script converts the alternative into explicit -or operators in the find command. You can modify the GNU script to do that. Or get gfind to work.
By the way, GNU's updatedb script builds a completely new database from scratch on every run, just like macOS's.
Your Debian installation is using mlocate which is a completely different implementation than GNU locate, not as widely ported, and not available on macOS AFAIK. And even though mlocate runs quickly on your Debian installation, that does not mean it runs a lot faster than GNU locate. Both run in under a second building the entire database from scratch on my Debian installation when all the disk metadata is in RAM (which is usually the case).
Apple provides mdfind, which uses the incremental database created by mds, which is largely triggered by file system events. This makes it (theoretically) much more efficient than even mlocate, which still has to traverse the entire directory structure looking for changed directories. The problem is that incremental builds accumulate errors. That is why locate, with its full rebuild every time, is still around and preferred by many.