Many conflicting views on this one, but your intended purpose helps the discussion.
Retro MTBs tend to follow the more "traditional" diamond pattern. You will find pretty much a straight and level top tube, and seattube frame size measurement will give an actual distance between the BB and the join in the top tube. Your standover height will be determined by the height of the top tube, no surprises there, and the length of the top tube will be more or less proportionate. So, if you ride a 21 inch road bike, a 21" MTB should be pretty close. As long as standover is sufficient you can tweak the top tube length with stems, saddle position and layback seatposts.
Modern MTBs tend to have a far more compact design, with sloping, swooping and sometimes even curved top tubes. Frame size based on seat tube measurements are less reliable, or are even quoted as "virtual". What's more, the geometry changes with different forks, some have long stretched cockpits, others encourage you to go small frame with long seatpost.
Intended purpose; well, if you want a short snappy frame to throw around off jumps and technical trails, or a long stretched out arse up head down XC missile, or a day long sit up and beg trailbasher, well, you may want to look to less conventional sizing. As you describe however, I'd stick with the frame that gives you a relatively long comfy cockpit.