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I have a experimental version of the DHTML exporter that does include toggle-able notes. The whole thing has been heavily restructured and I'm sure still missing things so I haven't released it yet. And I haven't had time to work on it since the iPad was announced :) But that will be coming.

Currently we don't have any way to handle export settings for XSLT based exporters so we can't offer any options like there is in settings or for printing.