1 - If you want to use
Desktop edition rather than
Server, it's up to you
Both work and if you are convinced difference is only GUI, then you're right, rather go for desktop edition. Differences in term of kernel settings are most likely not a concern for you.
2 - I though you wanted to install, based on your first post, "firewall" only, reason why I said "this is perhaps overkilling". If you want to also install LDAP and DHCP and some other modules, then Zentyal makes more sense.
There is one point I would like to highlight: it looks like you want to know the very detail of everything and look at Zentyal from the "low" side. Why not but keep in mind that Zentyal has been designed to be installed, configured and used through GUI, installing module rather than low level component. I refer here to your DNSmasq comment. With Zentyal, you do not install DNSmasq but "DNS service", no matters what DNS engine behind is.
If, for some reason, you don need DNSmasq, I would suggest not to go for Zentyal but rather build your own solution otherwise it can be quite complex to adapt to Zentyal.This aside, I don't understand your point with your ISP's DNS. Sorry
For what concerns user's home directories, I'm a bit confused too: is your point related to UID numbers and GUID numbers?