One fun example of this is the so-called RPM "5" fork[0], which is basically dead and almost entirely unused[1].

The result is the main RPM everyone uses will probably stay at version 4.x forever.

[0]: http://rpm5.org/

[1]: https://en.wikipedia.org/wiki/Rpm_(software)#RPM_v5

They could skip a version like PHP did. Among other reasons, since books and articles about PHP 6 had already been written long before PHP 5+1 came out, they went with 7.

Sure, they could. I don't think they've felt the need to. RPM tends to change slowly and conservatively.

Both Git and Linux are trademarked, presumably to prevent such hijinx

Linux is trademarked because of some "hijinx"...

"Initially, nobody registered it, but on August 15, 1994, [...] filed for the trademark Linux, and then demanded royalties from Linux distributors. In 1996, Torvalds and some affected organizations sued him to have the trademark assigned to Torvalds, and, in 1997, the case was settled." https://en.wikipedia.org/wiki/Linux#Copyright,_trademark_and...

Isn't it customary to at least rename the fork?

Customary, but unless the name is trademarked, not required.

Some licences require a change of name for substantial modifications, e.g. the Artistic Licence and Apache Licence v1. But those kinds of clauses are pretty rare nowadays.