It really sucks that every discussion of Clippy in Smash has to devolve into semantics instead of just... the character's merit. Nobody has these discussions about characters like the DSi budgie or the 100 Classic Books owl. Every Nintendo toy is completely unrepped in Smash, while Nintendo utility applications are well-repped. Utility software products are video games by Smash's own logic, I find it hard to believe it's a special Nintendo-only exception, because if Nintendo got exceptions like that, there would be Hanafuda and Ultra Hand content at least, those aren't estranged branches of the Nintendo "family tree" they're supposedly ashamed of like CDi and such, they pop up all the time in every other Nintendo game that uses nostalgia aesthetics. "Nintendo content can get this, 3P content can't" has always been something diminshed in every Smash game, and I think it's just right to assume that what goes for Nintendo - at least in terms of what source materials are included and what role they are given, if not individual depictions - always COULD go for Microsoft or Sega or etc - not WILL, I don't believe Clippy or Windows as a whole is remotely on Smash's radar, just COULD.
Additionally, I don't think Clippy is as inherently tied to Office as many people believe. Yes, that is the product he is from, but most people who know Clippy think of him moreso as a general image of Windows as a whole, not just Office. He has a similar "unofficial mascot" status to say, Mega Man, where he is treated as a visual shorthand for Microsoft and Windows, despite not officially being designed for or ever having taken that role.