Well of course, yes, getting what fits you best takes precedence over any number (except, maybe, cost!), and yes, some companies give sizes that aren't a measure of anything on the actual bike, and are rather "it fits like a traditional size 54cm" or whatever.

That said, actual measurements, like the effective top tube length you gave as an example between Breezer and Trek, should be measured the same way, e.g. center-to-center along the horizontal; I can't recall seeing effective top tube measured any other way.

To your point that there are a lot of different numbers flying around out there, yes, you're right about that. I think that once you get those most relevant to you locked in, though, it will be much easier to sift through the options. For example, it sounds like you like longer reach, so bikes with longer TTs are of more interest, but what is the # you're looking for, right? If you can determine its between 23.5" and 24", you can weed out the 23" ETT bikes even though they may be designated Medium or something else seemingly appropriate. Same goes for minimum standover height, though I think your distaste for low top tubes a bit strange.