I know you may think it’s stubornesss in the face of overwhelming evidence but... I still believe the measurement they give is for seat tube length or a guideline to seatube length.... I’ve just googled it a fair bit and I can’t find any source that says the size, for example 56, relates to top tube, effective, or actual top tube. But multiple sources that suggest it relates to seat tube. It’s possible that with sloping geometry frames they take a measurement as being the effective seat tube rather than actual height. And different manufacturers have different methods. I know you have numbers that suggest it does relate to toptube length but they’re not consistent across the range. For example the 49 tarmac has a top tube that’s just inside 52cm.
Can you find anything online that states frame size description relates to top tube length? I can’t find anything to suggest the 56 tarmac is measured from effective top tube. And I’ve personally never heard a bikes effective top tube being the source of its sizing number. Like I say I know the numbers seem a lot closer to top tube length than the seat tube so this whole debate may make me sound a little silly... it’s just I’ve always taken the size of a bike to be seat tube length. And nothing I’ve just read tells me different (other than the actual measurements!) I never actually payed much attention to it to be honest because I think it’s not the most relevant thing.
Either way... I think this conversation at least goes some way in proving that stack and reach are much clearer and ultimately more important overall, when choosing a bike frame than any one measurement in isolation.
I think you're absolutely right that seat tube length is the traditional way to measure a road bike, but this has become an almost meaningless measurement to use on compact frames with sloping top tubes.
I don't know what the 49, 52, 54, 56 etc sizes for Specialized actually relate to for sure (if they relate directly to anything!), but they have no relation at all to seat tube length, but they do have a vague relation to effective top tube, which is why I assumed this was what they meant (roughly!) by it. It's confusing, and probably why many manufacturers use S, M, L etc now instead. Cervelo for example size their bikes as 48, 51, 54, 56, 58, 61 which again vaguely relates to effective top tube (and a size 56 has 56.4cm effective top tube) but they don't even give a measurement for seat tube length on their geometry guide at all!
What it might be, is a bit of a tradition thing, where the size numbers now quoted relate to what an old fashioned racing bike with horizontal top tube would have been when measured by seat tube, and some manufacturers have just stuck to these size numbers, and it's just coincidence that they closely match effective top tube length? Bottom line is, check and compare the geometry, and compare more than one measurement as you say.
It's lovely to be back after not posting for a while and be straight into a deep discussion about frame size and geometry with you Tommy!