Find that domains.tpl was, infact, domains.conf.tpl. Anyway, there were some issues to be discussed (if MR wants, of course).
Found that
### MR -- disable perl until fix hardlinks issue
#ScriptAlias /cgi-bin/ "/home/<?php echo $user; ?>/<?php echo $domainname; ?>/cgi-bin/"
invokes cgi-bin using a /home/$user/domain.tdl/cgi-bin (and also, for subdomains, is my guess).
Some users (including me), uses a set of directories in their structure more obscure, to gain darkness over malicious users (i.e. mydomain.com often uses a ~myuser/alaksf/ for its domain root).
For this case used:
ln -s alakfs mydomain.com
and got no 404, but 500 error.
Any ideas?