There will be tons of overlap in open source software, always. No point in getting upset about it. Most of the time, the purpose of the software is completely different.
That being said, I think this is a good rule of thumb out of courtesy and good judgement, even if trademarks are not involved. It just leads to dilution of both brands/projects, if they are similar enough in what they do.
For this, I'm only aware of Mozilla's Project Mentat [1], but no problem there.
Quoting: "A Mentat is a fictional type of human, presented in Frank Herbert's science fiction Dune universe. In an interstellar society that fears a resurgence of artificial intelligence and thus prohibits computers, Mentats are specially trained to mimic the cognitive and analytical ability of electronic computers." [1]