In response to your acute observation regarding Autonomy rather than Independence (I've given them capital letters because I believe them to be subjects to teach like Maths or English or Geography) I would agree that they're different, but not necessarily mutually exclusive.
I think the act of being Independent is largely a series of skills taught and learned, as in dressing and undressing, teeth cleaning, showering, bathing, personal care, travel training, shopping, cooking, budgeting, cleaning, ironing, bed making etc etc. As such not everyone is going to be able to be entirely independent, and clearly those with PMLD may not get very far along the journey because of their profound physical and intellectual difficulties. Most with SLD and all with MLD should however be able, given time, resources and skilled teaching, to get quite a way along the journey. People will get as far as they can get depending on their personal circumstances. I'm a big fan of adopting a Capability Approach (Nussbaum, 2000, 2011) to education; that is, its role is to maximise opportunities for learners to do the best they can do and be the best they can be, irrespective of their abilities and disabilities.
Autonomy is however, much more of a process based operation. That is, the process rather than the product is the important thing, and the process is learned and understood by 'doing'. Rather like Intensive Interaction or more prosaically, dancing. One doesn't follow a set of instructions in order to learn how to dance, one dances. And the more one dances the more one learns how to. Autonomy centres around self-belief, self-confidence and self-esteem, all essential qualities which must be fostered as much, if not more than the skill of independence itself. There is no point in mastering anything if you believe you're no good, because if you believe you're no good, you won't be motivated, try, be ready to fail, take chances, and in the end you will be no good. Autonomy is a state of mind that all 'teachers' (many people are teachers without having the paper qualification) must do their utmost to foster, and I absolutely accept, not enough schools (both special and mainstream) spend time and thought on this. This is however, an essential part of the Equals Independence scheme of work, and indeed all of the other schemes of work (Communication, Thinking and Problem Solving and Play and Leisure) so far published.
Nussbaum M A (2000) Women and Human Development: The Capabilities Approach. New York. Cambridge University Press.
Nussbaum M A (2011) Creating Capabilities. Camb; Mas. Belknap Press.
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