Im not sure what you guys mean exactly... but, Allan does KNOW exactly what he is playing over each chord (or static vamp)... and does understand it from the perpective of "what sound am I playing over which chord"... having said that, he has totally different names for each scale, his own nomenclature... not sure that really makes a difference though, it still doesnt mean he DOESNT know what he is doing...
In fact, Allan indeed does know exactly what to play to imply which "sound"... he has his own names for each sound, usually calling scales by variations of alterations to the intervallic structure (as that column does)... but, he names them from a different perpective (watch his REH video)...
However, Allan when playing is approaching everything from an aural stand point, and he will play what he understands to be appropriate to a given chord (for a given sound)... it doesnt mean he is thinking "NOW I WILL PLAY THIS D PHRYGIAN DOM"... he simply chooses something from his date bank of information, and executes it (phrases it)... as he wishes.
Most players on that level, they simply PLAY, and what they have in their vocabulary will come out as they choose to imply a certain sound over a certain chord... to answer:
Allan does KNOW what he is playing, and is thinking of the possible things he wants to hear on each chord (or static chord)... but, he probably does not play and THINK aloud... "now this, now that..." It comes out naturally, through the years of playing, and the natural gravitation towards a sound...
Still, that changes nothing, the things FRAN has labelled is what he IS playing... in "our" musical language... and so, the theory works, Allan would know it all undera different name, but that doesnt really change anything... as "our" theory, and "his" theory... are the same things under different names.
If you were implying that he just plays by ear, and doesnt understand WHAT he is playing at all... then, NO... you would be wrong under that assumption. He does indeed know, and its simple... if you ask him what to play over a chord, he will give you countless scales which he would use... all of which come out of which alterations each would add to a given chord.