Rekrunner,
If you read some of my earlier posts you will have noted that I supplied a list of variables similar to your own. I am not arguing that Training Methodologies alone account for improved performances.
However, I think that you are being too kind to HRE ... he refuses to believe that 2-05 Marathons can be run by "clean" athletes .... he's been the guy who keeps harping on about PEDs & (by implication) suggesting that sub 2-05 Kenyans must be using EPO.
HRE (Richard Englehart) is a dyed in the wool Lydiard disciple .... nothing wrong in this ... I have myself described Lydiard Training methods as being the "gold plated" training method of the 1960s. Richard's problem, however, is that he cannot accept that modern training methods are "better" in terms of top class marathon performances.
On a more philosophical level .... I am not so pessimistic as you in thinking that the only way to compare these methodologies is to have A or B train different athletes to a certain level using different training methods. I believe that we can look at the essence of each method and say "this is good" or "this is not so good" ...
So, for instance, in looking @ Lydiard Methodology we might say ....
* Lydiard recognised the critical importance of aerobic conditioning @ a time when anaerobic interval training dominated training practice (this is good)
* Lydiard's classic method is too linear at a time (2010s) when there is an abundance of racing opportunities (this is not so good)
By the same token we could look at "modern" training methodologies as used by Canova and we might say ....
* Specificity develops the ability to prolong race pace (this is good)
* Canova's methods are too demanding on the novice runner (this is not so good)
It's this kind of analysis / debate we should be having BUT some people (HRE, for instance) would rather fly kites (PEDs) than enter such a debate.