I think you're missing some nuance here.
3DSen is based on reverse engineering and not IP since it's not selling the ROMs that come with it. All completely legal to sell and don't mind buying to support this guy's reverse engineering and transformation effort. If it was just some stock NES emulator that he was selling, eh, I'd probably just say legal but bullshit.
Lossless Scaling is a tool/actual framework that uses released/open source API calls to apply frame gen to any game, as far as I know and that's not violating any terms or conditions or IP either.
With this, while I can appreciate that he's done this for other game, the terms and conditions for them is "don't use our tools to sell mods". Do I agree with it? Actually yes, for the most part. I'm of the firm belief that the modding community should be open, I think that these are things that should be done for passion, I like having donations set up, and that we're lucky that we live in an age that many game companies are kind enough to release modding tools without demanding a license fee. Plus he's not selling a framework here, he's selling his framework built with a company's tools that says "No paid mods because we think the modding community should be open".
I think that IP is often tricky and I think that this is fine and not a slippery slope argument.