Can't rename /home/antony/perl/l.pl to /home/antony/perl/l.plsub/.bak: No such file or directory

If you pay attention to the error message, you'll see that the value of $^I is being appended to the file currently being edited. Yes, you can have a subdir where to save the backups (in this case, it would be named l.plsub but then you would need one directory per backup. Not much different from having the backup in the same directory as the file itself.