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 mynewsite.com in your Control Panel and point it to the folder of the main site
  3. create a sub-site new.mysite.com in the Network and use the plugin to map the domain mynewsite.com to it
  4. enable wildcard subdomains for mynewsite.com in Control Panel
  5. create a sub-site new2.mysite.com and map the sub-domain site2.mynewsite.com to it

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

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