It's an interesting question, but there's so many ways to parse it really does just amount to what your headcanon is.
I knew a kid who insisted Houndour was a Kanto Pokemon and, well, he isn't wrong – you catch Houndour near Saffron City in GSC, and it isnt available in Johto.
For the most part, I have tended to mentally associate Pokemon with the Gen they were first introduced in, with very few exceptions. It's really idiosyncratic, with no consistent rhyme or reason.
I never caught Horsea or Seadra in RBY, and their cards came out when rumors of GSC were already out there. That I only bothered with Seadra in GSC and evolved it into Kingdra, has ended up so that the entire line "feels" Johto to me.
Wynaut is altogether weird for me. I consider it a Sinnoh-mon, because it felt out of place in Hoenn, and seemed to fit in more with all the goofy cross-gens in DP.
Manyte is a Johtomon to me, somehow.
Roselia was an insignificant POS in Gen III, and is unique in getting a Baby pre-evo, and a Stage 2 evo, in DP. So it got entirely subsumed to me and I think if it as a Sinnohmon.
There are a lot of Gen V mon I consider Kalosmon (or even Alolamon, in some cases, if I never saw them in XY/ORAS) because I skipped BWB2W2. I don't have a mental running list, but e.g. Whimsicott is a Kalosmon to me, and I don't think it really is.
