The first of your hypotheses is correct. For saturations below "fancy light", GIA takes the position that there is not enough colour in the stone to be able to assess its distribution reliably, and thus does not grade it. Hence the "Not applicable" note. If the distribution of colour is not even, GIA will note it as "uneven" - see this one as an example

As far as I know, the owner has no option to ask GIA to omit or include certain information; the only "getaway" is to order a type of report that does not include certain information (e.g. the "Color Origin" report has no clarity or finish grade)