As to mastering content with InDesign to support output of ISO 14289-1 (PDF/UA-1) compliant PDF (aka "accessible PDF) you'll want to ask at the InD user-2-user forum.
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http://forums.adobe.com/community/indesign
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Aside from making use of ISO 14289-1 (the ISO Standard for what is an accessible PDF) and ISO 3200-1 (on which ISO 14289-1 is based) there are other essential references available at AIIM.
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http://www.aiim.org/Research-and-Publications/Standards/Committees/PDFUA
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These are:
PDF/UA-1 Technical Implementation Guide: Understanding ISO 14289-1 (PDF/UA-1)
PDF/UA-1 Technical Implementation Guide: Understanding ISO 32000-1 (PDF 1.7) (under development)
Achieving WCAG 2.0 with PDF/UA
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What happens in InD does not 'lock down' an output PDF as accessible (PDF/UA-1 compliant); no more so than if you were to master content with FrameMaker, MS Word, Notepad, or something else. Certainly much can be done while mastering content in an authoring file to support PDF/UA compliance. For InD Adobe has informative articles in their 'InD web space' and at Adobe TV.
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Be well...