I have a Spec Roubaix that fits me like a glove. I'm quite pleased with it, and i would like to make sure I select the right size as I look for CX and/or Gravelcross style bikes that simply aren't in stock.

As it stands, I'm 5'9 with stumps for legs and arms, but I have a long torso, and my Roubaix 56cm fits great. Usually, a 5'9 guy gets put on a 53/54, but my disproportionate torso length seems to agree more with the 56cm.

The Roubaix's measurements are 387/589/798 for reach/stack/standover. if I find a bike size that replicates those 3 #s fairly well, am I reasonably well-assured that I'm selecting the proper size bike for my weird-shaped torso/arm & leg length? Perhaps I'd need to adjust the stem length or spacers or whatever, but if I'm going to have my LBS order me a noble steed and I need to determine which size to request, are those the primary 3 #s I need to try to get close to? Now, I know things like chainstay length and wheelbase as well as BB drop have huge affects on handling, but purely for fit and especially sizing purposes, are stack, reach, and standover "the big 3"?

you'd want the seat tube angle to be similar as well, though small differences there can be adjusted for by moving the saddle fore-aft. Also, differences in set-back of seat post can affect things, but seat posts can be changed.

I would have to say "no". As you just observed, different bikes can have different BB drops which would make standover height an irrelevant criteria for "fit". YOUR dimensions are what is salient for fit and you have not supplied those.

I would say stack, reach and saddle setback relative to the BB plumb line. If stack is good, standover really shouldn't be a problem.