Is it possible to put a site other than #1 as a Multisite top-level domain?

I’ve never changed the main site URL (scenario 1), but I know it’s possible: three relevant links found in a quick search.

For the second scenario, although not optimal, the standard procedure applies:

  1. install the plugin WordPress MU Domain Mapping
  2. park the TLD in your Control Panel and point it to the folder of the main site
  3. create a sub-site in the Network and use the plugin to map the domain to it
  4. enable wildcard subdomains for in Control Panel
  5. create a sub-site and map the sub-domain to it

All the mapping process is well explained in the following tutorials: