No great conspiracy here. Any mid to large org maintain such lists. If you fire someone who is wasting the orgs time, do you then want him to show up/get hired/be entertained by some group in the next building/next campus etc who have no idea what the story is?

The guy is not an ex-Google employee. This event was named in the Damore lawsuit as evidence of discrimination against political views because all he was guilty of was blogging things someone at Google had a problem with.

It doesn’t make you uncomfortable to know that even if you’ve had no previous interactions with Google, you may be tracked and added to a list of undesirables? Who controls the list, who has power to add people to it, and what else are they doing with this list? What if they’re looking at his search history too? Would that be okay?

Google are a private company with no requirement (barring legal strictures) to allow anyone onto their campus. If they want a list of undesirables, they can have one. Same as you've probably got one for your house.

As long as the list is used for "people who will/won't be invited to speak at Google HQ", and not used to influence search results, I have zero problems with it.