Following this logic, does this mean if I have a project name like ABC, and some company decided to incorporate in this name plus registering the trademark, I have to give up the name when they decide to come after me? Like I have a github.com/ABC, a npmjs.com/org/ABC. All just gone, because trademarks right gives them the right, and I have nothing that protects me?

If that is the case, ok. It's just that I was naive enough to believe I could protect my little open-source project from this using a trademark. The EUPIO somewhat confirmed in their writing that you don't need commercial activities, but you need "genuine use", which is, again, hard to prove if you don't collect user data.

"ABC" is already a trademark. There's probably dozens if not hundreds of trademarks for "ABC".

Trademarks are only the right to use a name commercially for a particular good or service.

Anything outside of that is fair game.