I agree with you. They don't actually have two World titles. The title that the Yeet guy won is called a "World" title, but it isn't positioned as one and I assume nobody views it as such. It would be like saying Chris Benoit was World Champion in 2000 when he held the IC title. They seem to be positioned similarly.
The purpose back in the day for two "World" titles was because House Shows were big business, and they felt having a "World" title match on a house show actually still mattered in the 2000s. They did eventually go with split brand PPVs for a series of time, but if I recall live events were the logical reasont to originally have two champions. I don't think they do House Shows anymore on anywhere near the same basis assuming they do them at all.
I don't think it has ever worked in WWE. It was always very similar to how the TNT or whatever the titles are called in AEW now were treated. Where you'd go a year with the title not mattering because a scrub holds it, then they would put it on the Undertaker and it would be a World title again. This was usually with the title on Smackdown.
I get that shows like WrestleMania are built on "supercards" and historically there have been attractions pushed bigger than the world title (McMahon/Hogan, Undertakers streak, etc) - but it's comical how the secondary World title is often 4th, 5th or worse from the top when you line up the positioning of the top matches. I don't watch Raw or Smackdown, but I assume Yeet guys world title program wasn't the A story on whatever show he is on.
Fans aren't dumb, so they can perceive when a guy is actually positioned as a top guy and when it's a fake top guy where they have Michael Cole say YEETGUY IS AT THE TOP OF THE BUSINESS but the show revolves around what Paul Heyman ate for lunch, and Yeetguy is running away from Kane in his first post WrestleMania program.
If they are invested in Yeetguy, he should have closed night 2 with the win. If he is not a real top guy, which is what it seems like, then whatever. The problem is that they had two main events with run ins and shocking finishes like they were running the ECW arena in 1995, and you obviously can't do the Heyman turn in the middle of the card and follow it up with basically a midcard title win (Yeetguy winning).