Sega doesn't want to preserve the ownership of their ip, they were bought by a gambling company who took on their name and is using sega as a public relations shield.
Their aim is to keep sega in high public esteem.

Meanwhile Nintendos ip is extremely valuable compared to the size of their company, so their aim is to protect ownership way more than making new games or other ongoing business.

International ip law is weird, so letting fanmade games go runs a risk of loosing ip. For Nintendo that is even more dangerous than for other studios whose ip value compared to revenue is not as extreme. While for sega ultimately loosing ip control is basically the point of the investment.

Sorry if I missed a tiny bit of context: most Sonic stuff is SoA lately, especially after the success of the movie. SoJ is a lot less open minded.

I don't get why Nintendo of America isn't as cool, though. I'm betting Japan dictates a lot more with them.