Its an interesting observation.
I suppose that at a certian level of fandom it can become, for lack of a better comparison (and not trying to start any horrible debates), kinda like a religion...and (at least in my experience) you wanna personalize what you believe in. (and I am not saying I suscribe to the church of the TMNT

)
myself, like most other fanfic writers, create my own reality for the turtle. I prefer the mirage/new show turtles so they tend to be more along those lines...I do not like all the science fictiony stuff so mostly all my stories are urbanized...and I do not like turtles fallling in love with people, so I leave them as loners only really relying on eachother....
Of course, that does not mean I do not appreciate the cannon stuff