I could be wrong, but seem to recall seeing that the manufacture of some, or all of E.C. in recent times, has been made in Czechoslovakia - or at least not in the U.K., as mentioned by Sue. I have a feeling that some glass I've seen recently uses the backstamp of 'E. C. International'.
The backstamp for E.C., post WW II, included the wording 'MADE IN SCOTLAND' - this was a standard backstamp that existed until probably some time late in the C20/early C21, and if that wording is absent then it is unlikely that these glasses were made in Scotland.
Individual variation between identically patterned glasses, may have been more usual some years back when hand crafting glass was more the norm, but with modern production methods, I can't see the reasoning behind the sort of differences the op mentions. Traditional hand skills in making three part drinking glasses shouldn't have changed, unless we are speaking of cutting corners, or making to a different specification.
We don't know for certain, but if it was the case that these glasses are missing the backstamp, because they are seconds, then the op might have a case insofar as seconds were not discussed, or ordered.
E.C. were always known in particular for hand crafted cut lead crystal glass, not for pressed glass - certainly drinking glasses made by them in Scotland were not made by pressing.
"Had you been aware of how these vary etc"., is a non starter of an argument, since had you been aware of the difference then obviously you wouldn't have ordered them.
At least the op should request information from the seller to support the contention that these were made in Scotland, as apparently claimed, and not elsewhere, particularly as there is a lack of backstamp.