It is possible but very unlikely.
According to this interview the author, Stephen Chbosky, based the character of Charlie on himself, and some of the plot on his own teenage years in Pittsburgh.
SM: How did your personal experiences translate into the film?
SC: There were certain years I remembered very well. I remember in 7th grade, I was painfully shy and didn’t venture out of my shell very often, even though I desperately wanted to ... Charlie was just an expression of how I felt deep in my heart – observing everyone and everything and really just wanting everyone to be happy.
I can find no mention of any of these diagnoses applying to Chboksy himself, so if he based Charlie's character on his own, it would seem vastly unlikely that he intended to portray Charlie as being on the autistic spectrum.
It is also worth noting that, while Charlie has some social issues, he is also empathic and sensitive to the emotions of others. For example, his appreciation that Patrick's romantic moves toward him are motivated by being on the rebound from his relationship with Brad. Also, note in the quote above that Chbosky claims Charlie is "observing" everyone and wants them to be "happy." These are, if anything, the opposite of what one except to observe of someone on the spectrum.