I use a home-brewed cosmology for the campaign I DM. Some people (mainly clerics and churches) in the game world actually use the "Great Wheel" Cosmology, but they are wrong.
The druids came up with the most correct version (the "Source to Terminus" cosmology I wrote up), and various wizard schools are split between the Great Wheel Cosmology, the Source/Terminus, and other theories.
My cosmology is mostly the 2e version, with the 5e additions tacked on, but people on different worlds, and with different levels of knowledge have all sorts of different ideas. So priests in the Forgotten Realms believe the cosmology in the 3e FRCS, people with just a little bit of knowledge believe something like the 1e Manual of the Planes "Happy Hunting Grounds" and all, but minus quasi and para elemental planes, scholars tend to believe something like the setup in the 5e PHB, but don't know about the Border Elemental plan regions, and people living out on the planes in Sigil or wherever have the most accurate view (2e + 5e additions). That basically holds true for most worlds--priests tend to believe in the more particular cosmological arrangement that is part of their world's mythology, while educated wizards disagree.
On worlds with very different cosmologies, people might not have any idea of the Great Wheel in any form, and have a totally different conception. From their point of view it works just as well, even if from other points of view their "heaven place" is some domain on Elysium, and their meeting place of the gods is a demi-plane or some domain out in the Hinterlands of the Outlands. Since people on a particular material plane world generally only interact with small parts of the cosmos, the nature of most of it is both unknown and irrelevant to them, so they create less accurate but more mythologically consistent versions to believe in.
It's great fun for me to watch as the DM where my player's low-level characters from different worlds (Toril, Oerth, Krynn, and a couple of homebrews) were thrust together and eventually led to some in character discussions between the more knowledgeable characters about their different views of the multiverse. I had previously written a document for each player telling that in general what their PC knew, and the player with the Toril character had more out of character knowledge that was perfectly appropriate to use, making for a really fun session. Through divinations from a cleric of a power of Knowledge they were able to verify that the Arvandor known to the people of Toril and the 2 homebrew worlds (the character from Oerth just wasn't well versed in all this magic and relgion stuff) was the same place, which gave them some sort of connection amidst the confusion.
So I definitely agree with your methodology of having some people just have incorrect beliefs about how it all works.