They really aren’t much different technically. I’m going to assume what they mean by modern site collection is a group connect site collection.
So it breaks down to those being a normal site collection that has many products tied to the site collections document library. And security by default is tied to the site so that any owners in the attached group are site collection admins and members are part of the members sharepoint group which can be tweaked.
Modern is just a term for the pages or rendering technology the site collection / libraries use. It’s made up of spfx web parts etc and none of the old web parts will work on them.
Everything they say is flat because Microsoft and the new rexommenddd way of doing things is all site collections which essentially makes it flat. You get around that flat by creating a hub site which is turning a site into your parent site collection per say then you can join other site collections to this hub and it inherited theme and nav from the parent making it act like a sub site.
Communication sites are just modern only style classic sites that have a different top navigation template and many of the features turned off by default but it’s Basically a classic site collection with modern UI on by default and usually used when you want a site not connected to a 365 group.
