as I understand it 'reach' and 'stack' came from the mtb community, in an effort to find some std reference for the many variations of frame specs. Much of this was to allow riders who either wanted to have a reference for point of balance for climbing and especially for DH, while off the saddle.
http://www.pinkbike.com/news/08ReachStackStandard.html

Then, I guess the Tri crowd found it a good way to get some same std for their spec-ing...
http://www.slowtwitch.com/Bike_Fit/C...er_One_95.html

these dims do eliminate ST angle and BB, but just because they do, not because they actually take those into account. As you say 'stack' can vary without affecting reach.
BB Drop/height has an affect on bike handling and has always been a consideration in frame design, as relates to those intangible qualities of 'ride' and was always a discussion when it came to 'English' vs Italian and French, back in the day. The fact that is rarely mentioned in rider discussion is that TT clearance is almost never an issue these days and relating it to a 'road' position serves only to confuse most, and is predetermined once you pick a frame.
And even though some think STA might not be important, other than provide the right setback for a given rider/leg length; it does have an appreciable affect on the 'ride' of a bike (for which I could give numerous examples).
In all I find stack and reach to be just another set of numbers in the roadie world, which promote no better understanding of the overall package. Ultimately you have to pick some reference points to do your setup (if you know what you're doin for yourself...) for which someone could include stack and reach or just call it TMI.