Because there is literally zero evidence for it.

"Raticate is missing when Blue shows up in the Tower, ergo Raticate must be dead" is a dumb they considering that he was trying(and failing) to catch a Marrowhack in the tower and that we know for a fact that he doesn't use all of th Pokemon he has and has access to a storage box in the PCs.

There's also the simple fact that literally no Pokemon ever die in battle anywhere else in the series and there's nothing differant about any of Red's batles with Blue.

It's a fanon hat exists solely to make Red less perfect, Blue(the guy who was willing to let terrorists control Saffron city when he could have saved the day just to fight you) more sympathetic, or make the game darker than it already is.

You're attaching unrelated phenomena together to create a story that doesn't exist.