Much of the research on autism is based on studies using high-functioning autistic (HFA) subjects. Thus, much of our understanding is based on that "subtype." A sizable proportion of individuals diagnosed on the spectrum will be pragmatically classified as having low-functioning autism. They may not ever develop productive spoken language or use vocal communication in a highly idiosyncratic way. They may score in either severe or profoundly MR/ID range, yet the quality of their cognitive aberrations suggests a way of thinking that can't be quantified in a traditional manner. The likelihood of regression (linguistic, motoric) is also far more likely and as their cognitive deficits increase, so do their chances of developing persistent epileptiform disorders. Is it time to entertain the idea that they are anything but "on the spectrum"?
Brian, I don't have an answer as much as more questions. This seems related to the decision of the working group that proposed to just have one "diagnosis" of ASD in DSM-V. So it seems like the trend is away from diagnostically "subdividing" individuals who exhibit symptoms that we currently associate with ASD. We know there's a lot of heterogeneity, including all the factors you mention that are more likely to be observed in individuals with autism who are more intellectually disabled. But if we say these individuals should have a different diagnosis, what criteria do we use to create a meaningful diagnostic category? Are we looking at characteristics that have a continuous distribution, or are we looking at characteristics that are discrete? Or maybe a combination of continuously distributed characteristics and discrete characteristics?
I agree with you that we cannot assume research findings related to ASD that come from participants who are high-functioning will generalize to those with severe intellectual deficits. And the occurrence of epileptiform disorders suggests some differing underlying biological mechanisms--but are these "added to" biological mechanisms underlying the expression of ASD in high-functioning individuals, or are the biological mechanisms completely different in individuals with high-functioning versus low-functioning ASD? These kinds of issues seem especially important in the quest for biomarkers that might guide targeted treatments of the core symptoms of ASD.
Another non-answer to your question that nevertheless seems related to the issues you are raising is that in 2010 the Interagency Autism Coordinating Committee called for more research on nonverbal, school-aged children with ASD, especially intervention research. Officially, the need was identified at an NIH-sponsored workshop on the topic, but my impression was that NIH sponsored the workshop in response to considerable input from parents and other stakeholders urging more research to address the needs of these children.
Considering that many autistic people are suggesting that high and low functioning are not actually useful distinctions, the whole HFA/LFA thing needs a LOT of work. Since autistic people from both groups note many commonalities (ability to speak and ability to communicate are not the same, and many autistic people do learn some form of communication, spoken or not) the idea that LFA is something other than autism seems unlikely. That those classified as LFA have more going on than just autism, however, is worth considering.
For the issues with the use of the distinction as done currently, I note "I am Joe's Functioning Label" (http://aspergersquare8.blogspot.com/2008/03/i-am-joes-functioning-label.html) and "Non-Speaking, Low Functioning" (http://www.shiftjournal.com/2012/01/11/non-speaking-low-functioning/) as two relevant articles, both written by autistic people, the second by a non-speaking autistic person who also has epilepsy, cerebral palsy, and possibly intellectual disability. One talks about issues related to being considered high functioning, the other about being considered low functioning.
The first comment here notes that functioning levels not being static is at the least possible, written by someone whose level changed with time. http://www.autismwomensnetwork.org/article/static-bubbles-myths-functioning-labels
The assumption ping pong page by Amanda Baggs also notes that not fitting into any one nice box is a thing. http://ballastexistenz.wordpress.com/2006/03/10/lets-play-assumption-ping-pong/
What are we trying to accomplish here? Is it about the actual needs, which vary hugely between people, regardless of functioning label, or is it about putting people into nice boxes? If it is the first, functioning labels are not very good at telling people what the actual needs are, and the second isn't going help the subjects of the research in any way. ( http://autisticadvocacy.org/2010/05/a-true-story-and-a-little-lesson-about-functioning-level/ and http://yesthattoo.blogspot.com/2012/05/functioning-labels.html may also have some relevance.)
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