Dave,
I really don't see the extra datum references as an issue it is a you are describing a complete framework, similar to what is required to measure parts on a CMM I believe the machine wants a complete reference framework (inspection guys?) set up first. If you end up not using all of them it is no real loss. This is the kind of compromises you get with general tolerancing, the standard itself, for many revisions (82, 94) has recommended a similar note for establishing dimensional controls in the past (section 4.4, NOTE).
Frank