I don't think he's referring to an internal Intel 64-bit project that wasn't known about. More likely he's referring to the already known Project Yamhill, which was about re-implementing AMD's extension as a backup plan.
To recap: Intel's focus on Itanium over x86-64 was a strategic decision that ultimately backfired. AMD capitalized on this by developing and documenting their 64-bit extension for x86, which quickly gained industry support. Intel, meanwhile, was reportedly working on "Yamhill," a secret project implementing AMD's architecture but initially disabling it in their CPUs.
The Quora comment by Robert Colwell suggests internal conflict within Intel. It implies that Intel considered their own 64-bit plans but ultimately followed AMD's lead. Colwell's phrasing, such as "our own internal version of x86-64," may reflect Intel's reluctance to fully acknowledge AMD's pioneering work, perhaps due to corporate pride and the failure of Itanium. There's also other phrases that seems to suggest Intel was making its independent 64-bit extension - e.g. it talks about " I decided to split the difference, by leaving in the gates but fusing off the functionality. That way, if I was right about Itanium and what AMD would do, Intel could very quickly get back in the game with x86". It makes it sound like AMD hasn't even moved on 64-bit and they are just preparing for this... even though the truth is AMD had developed the extension, released the spec and was releasing products with it, while Intel was busy with Itanium.
Colwell's choice of words could be influenced by Intel's culture, which might have downplayed AMD's role. While the comment might imply an independent Intel effort, it's more likely referring to their adaptation of AMD's successful architecture. The reluctance to openly credit AMD might stem from Itanium's failure and the fact that Intel's next step in 64-bit computing wasn't their own design but an industry necessity. I also think some of the wording comes across as personal arrogance - I doubt the decision to make a backup plan and leave the gates in were just up to one person, almost doing it contrary to orders by management. While I would buy (I have no idea, I don't know him) he might have had a significant role in making the backup plan etc. and advocating for it, it is likely not a case of one person just making this decision contrary to management, and chaanging some lines in VHDL to fuse it off, as it sounds like.