Nothing has stated it's the comics mutliverse that it connects to at the end of Loki just that it's connecting to new branches. Also them stating the MCU is Earth-616 in a film is them in fact disputing that it's Earth-199999. If they considered it Earth-199999 they would've said that but they didn't. Like it or not we have two offical Earth-616s now and they clearly aren't the same. They are two different multiverses with the only connection being one is an adaptation of the other.
Marvel doesn't consider Earth-199999 an alternate MCU like you're suggesting. They consider it the exact same MCU that this timeline is based on. If the MCU is officially considered Earth-199999, which it is, and Earth-616, which it is, then logically it has to do with the branches and pre-existing universes in Loki. You can't just pretend that the MCU isn't Earth-199999. That's an established canonical fact and it doesn't matter what this movie calls it.
What If...? is the multiverse created from those branches. It is what you can call the MCU's multiverse due to the events of Loki.
We know that universes exist that were unconnected to the "sacred timeline". Kang stated he "isolated" the MCU from the multiverse, not destroyed the multiverse. Obviously, the multiverse that he was talking about must be these unconnected trees. At the end of Loki, the MCU's branches connect to pre-existing realities that are not branches of the MCU, the only explanation is that that is the Marvel Multiverse. I'm sure that was the intention because it means that they are able to craft their own multiverse so to speak without stepping on the toes of the greater Marvel Multiverse.
Basically, the MCU, What If...?, Sony's Spider-Man Universe, Raimiverse, Webbverse and the Illuminati's universe are all part of the branches seen at the end of Loki. All of this MCU multiverse stuff is connected to that, and yes, the MCU is Earth-616 here.
The comics are their own part of the multiverse with their own specific branches. They are the closet to the "core" part of the multiverse. In fact, because they haven't been isolated from the rest, their numbering designation is the most "true" if such a thing exists.
But all of it is the same multiverse until EXPLICITLY stated otherwise.
Reminds me of when Smallville called their reality Earth-1 and the Arrowverse called their reality Earth-1 but it turns out the people in Earth-167 just had less understanding of the multiverse. The Illuminati most likely can't see beyond the "MCU Multiverse", so their Earth-616 is the MCU.
I'm trying to tell you that it is the same multiverse but actually isolated from the other realities.