What I propose is not to alter the current AST JSON document but to add a second JSON document after it containing the filter options, each terminated by its own newline.
As for specifying the filter which the option(s) belong to explicitly I think that is pretty much necessary to avoid confusion. Alternatively the `-F` option might be altered to take an optional 'value' which would be the options to the filter specified as 'key': `-F FILTERNAME[=FILTEROPTIONS]`.
Another question is whether the filter options should be parsed by pandoc or that should be left to the filter. At least perl and python already have libraries which can parse options from a string. Other filters may wish to receive their options e.g. as a JSON object string, since any filter has to be able to decode JSON.