The site only knows what the individuals at it know. Also, being on the 2600, I doubt it looks close enough to, or stage design even begins to resemble, an official game anyway.
I can't recall anything, but has Sega ever gone after emulation? I mean, a former employee made an emulator, that hasn't updated since he was re-employed in 2011, and still seems to be standard bearer for Genesis emulators so far, despite how outdated it is with modern Windows OS's(you need to checkmark a box in the compatibility options to be allowed to go full screen on some systems). I know emulators themselves(and patches) aren't the issue, so much as the roms are, but I don't recall Sega caring about rom sites(possibly because Saturn emulation would have been impossible at the time).
There's a Youtube channel I watch every so often, and when they talk about gaming, they actually say "Sega is notorious for shutting down fan projects" while giving 2 examples, and I'd never heard of the Phantasy Star one. The other is the obvious, Streets of Rage Remake. That's one of the oddest cases though. Bomber Games wasn't exactly hiding what they were doing for 8 years, and as I'd heard, even had contact with Sega the whole 8 years(I doubt you'd get the story from either side though). They put out a 4.2 and nothing for years. 5.0 comes out, and a week later comes the DMCA. Has any project Nintendo shut down made it past a day or 2 beforehand, let alone a week? Then, this November, the game had a 5.2 update. DMCA'd projects aren't typically allowed an update. (that said, at least someone cared enough to make a fan game for a series that could use a new game, instead of the usual Pokemon, Mario, Sonic, etc.)