Right, I got that you use domain mapping. That's still an optional plugin. You don't have to use it, and you don't have to use it for all the sites on your network.
No matter which way, this is still incorrect:
the administration interface needs a main domain distinct from the other domains.
That may be YOUR requirement, but it's not WORDPRESS's. It may look that way with domain mapping, but realize you're mapping the SUB sites, you can't map the main site. Also you can (if you want) use maindomani.com/subsite/wp-admin instead of subsite.com/wp-admin. So ... options :)
If YOU need multiple domains, then you pick one to be your parent site. That's all. The parent site would be the one your cpanel host is pointed to, and where you'd run domain.com/wp-admin/network . Then you make children sites as you need them.
But if you only need ONE domain, then you don't use domain mapping at all.
It's not that hard. One domain is the 'main' domain, using the main site. Other domains are children and are mapped for the sub-sites. That's it. Don't overthink it :) You don't need multiple IPs, and phpmyadmin would work off domain.com/phpmyadmin, same as always.
WordPress can totally handle 300 blogs with 3k visits a month. The architecture, I assume you mean server specs?, depend on how true your stats are there, and how many plugins (and which ones) you use. I'd start with an entry level VPS and go from there as you grow.