I doubt you'd be comparing apples to oranges over a long timeline. Actually, I don't think it's a slam dunk that we have more autism today, or more diagnoses.
It is interesting that these sorts of articles ("BPA exposure associated with 7 point IQ decrease" was a recent one on the HN front page) seem to gloss over the fact that when these exposures were higher, the Flynn Effect continued unabated. Lead is another substance that, although nasty, is blamed for IQ declines, yet, when lead levels were highest, average IQs continued to rise. Now that lead levels are plumbing new lows, is there evidence that those "lost" IQ points have been gained by younger generations? If BPA is banned, I am sure that there will be scant evidence of those 7 IQ points coming back in a generation or 2 (if anyone bothers looking). Your point about inter-generational autism rates is similar.
I'm not an expert, but I can't take these sorts of environmental toxicity studies seriously anymore.
In other words, even if rate of incidence is declining, rate of diagnoses has sharply risen in recent decades, complicating the data.
That's not correct, this research says nothing about other factors that could affect the rate of occurrence of autism.
I think it's safe to say, that, in the West, air pollution has dropped dramatically: https://en.wikipedia.org/wiki/Great_Smog