Except it was still the SAME UNIVERSE; just at a different point in time in that Universe. Thanos didn't travel to a completely different Universe in Endgame unlike Ultron in this What If episode.
Uhh, you're positing a dichotomy that doesn't exist. The entire defining premise of
What If...? is that these are alternate
timelines, versions of the universe where a specific decision was made differently and a new timeline branched off from that point forward, as seen at the end of
Loki season 1 when the branching of the multiverse was unleashed. The 2014 Thanos
was from an alternate timeline, a timeline that diverged when the Avengers came back and started altering events -- which, of course, was what allowed that alternate Thanos to become aware of their existence and travel forward to the future of their timeline. That was an alternate timeline from his perspective, because it was a reality where he had
not traveled to the future in 2014 but instead had waged the Infinity War, caused the Snap, and been killed nearly a decade later.
Fiction has a sloppy tendency to use the words "timeline" and "universe" interchangeably, but any version of reality that includes Earth, humanity, and specific individuals and events we recognize can only be an alternate timeline of our universe, a branching off from a common origin. A literally separate universe would have no familiar stars, planets, or people, and might not even have the same physical laws that allow planets and life as we know them to exist.
Also, in thinking about it further the series
Loki gives the answer and the answer would be
no infinity stones don't work outside their originating universe as the Time Keepers were using them as paperweights and they had no power whatsoever in the pocket universe 'He who I will call Immortus'

set up for the Time Keepers (before Loki and Sylvie ended that setup).
Which does not make sense because it contradicts
Endgame. Maybe the Stones just didn't work in the out-of-time pocket universe. That doesn't prove they wouldn't work
anywhere else, especially since
Endgame proved that they can.