The problem isn't really that DirectAdmin can't handle it, but that you use a slave nameserver which doesn't work the way the RFCs specify.
Yes, and no. It simply refuses with "Query refused" message if the zone you're asking for is not in the .LT domain registry and does not have ns2.domreg.lt listed as a slave NS for that zone. So naturally third level domains are not listed in registry, since in .lt TLD you register only for second level domains.
It is that way so domain owners who can't afford a real slave NS would be able to use this DomReg (.lt domain registry) provided slave NS. Which is our situation - we can't afford a real slave NS on a seperate physical location.
If DirectAdmin didn't touch the records it couldn't very well manage them.
Well at least there could be some kind of special block comments for parts which DirectAdmin should ignore. I'm not sure if bind zone files support any kind of comments, but if it does it would be rather straightforward to implement it so that it would ignore part of file between 2 special comments.
I'm not sure how that's specified in the RFCs, but I prefer creating a new zone if I'm using more than an A record; it just makes things easier.
Normally I also prefer that, but thing is that in this case I need only an MX record for that subdomain, which is just yet another service for the main domain (like
www.foobar.lt. for web, ftp.foobar.lt. for FTP and lists.foobar.lt. for mailing lists) it's just that this service (mailing lists) is handled by external server and also obviously requires not just an A record, but an MX record. So creating those MX records in the foobar.lt. zone is kinda logical and doesn't brake the one-zone for one-site logic about which getUP is talking, since it's yet another service for the same website.
The admin can create a new zone without creating a domain or a subdomain, but then only the admin will be able to administer it, so it doesn't really help you with what you want either.
Well the user won't be able to administer this zone (list.foobar.lt), but atleast it will be able to administer foobar.lt zone normally, as opposed to this "immutable flag" solution