It's the Same company, but that doesn't mean that Nintendo/Sakurai will discuss with all of the Company in regards to Smash. While owned by the Same Company, Id Software, who makes Doom and Wolfeinstein among others, is not the Same as Bethesda Game Studios who make the Fallout and Skyrim Games. It's the same with how Rare is Different from Mojiang, or How Atlus is Different from the Team Sonic branch when it comes to Discussions. Now in the Situation with Rare and Mojiang, we See Nintendo talked to Both since Both Banjo and Steve are in Smash, but that doesn't automatically apply to Id Software
The Doom Creator was talking how they Approached Nintendo, it did not went anywhere, and seeing how this interview was 3 Days before Byleth got in, it seems there wasn't anything else that happened in regards to FP2, since it was finalized around November. If there was more talks, I doubt they would go into detail about how they weren't Approached, and they Approached them, and they went nowhere. they could and would have picked better wording. People under NDA don't usually go into detail like this unless either after the content they got is revealed, or there is nothing in the game at all. I've seen Deflections like with SNK talking about the Dog, or Grant saying don't hold your breath, and etc, but they never went into inside talks like this. If there is another example like this though I don't know and I am willing to be proven wrong
For another reference, Here's Shanate's Creator talking about Shantae's Spirit in the game
In Shantae creator Matt Bozon interview, learn more about the latest game's design, past games, and how "Shantae needs an anime."
www.siliconera.com
Nintendo never Approached Matt from what it seems like, they just sent Nintendo some artwork of Shantae and hope they be in the game, and that's how they ended up as Spirit. in any case, they Zipped up and didn't speak too much on it, and only went into the whole process of everything after Shantae's spirit was revealed.
Discussions around Spirits and Playable characters are wildly Different, but If Matt did not Speak intrcatally about the whole Process for a Spirit, I doubt Doom Man would do actually do that if Doomguy was present in Playable form. yes