Because despite it being an alternate universe within the original HM canon, anytime one of those characters show up in a later game...

... they're visiting from Mineral Town, the BTN setting, and not Flowerbud Village, the HM64 setting.

And BTN has been ported twice, while HM64 has never been ported.

I do admit I find BTN to be the better game in the BTN/HM64 debate (though I may be nostalgia blind, I didn't play HM64 until later)

But HM64 is a direct sequel to the original and keeps canon in tact. In that respect, BTN reads like fanfic.

"Let's redo ALL THE FAMILIAL TIES and ALL THE PAIRINGS"