Using janet-v1.38.0-linux from the github repo installed for the local user.
Then PREFIX=~/janet janet bootstrap.janet:
error: Permission denied: /usr/local/lib/janet
in os/mkdir [src/core/os.c] on line 1986
in create-dirs [jpm/shutil.janet] on line 106, column 27
in generate-config [jpm/make-config.janet] on line 54, column 7
in thunk [bootstrap.janet] (tail call) on line 25, column 24
It seems /usr/local/lib/janet is hardcoded in and ignoring PREFIX.