This isn't the issue. Neo4j didn't violate FSF's copyright.
You distribute your top level license that includes the original text of AGPL alongside some additional restrictions. This is a 100% expected thing to do. The original license has in section 7 a permitted set of restrictions, and then a clause saying that if you find any other "further restrictions" you can strip them out.
The problem is that Neo4j actually did that -- they added an "other further restriction", and someone went and distributed a version with the restriction stripped out as the license says they are allowed to do.
Neo4j could have distributed a version of AGPL with section 7 modified -- but then they actually would be violating the copyright on AGPL. Alternatively they could have written their own license, but then they'd have to pay lawyers to write a proper license that properly expresses what they want which is tricky/expensive to get right.