Well, I don't view it just as a dismissal because I'm actually quite impressed he noticed not being able to hear the pedal tone in that one section. I'm just saying it's quite small potatoes compared to the bigger picture. I.e. clear recording, nice editing, as well as sound playing (there aren't any mistruck notes!), etc., - I've actually learned these bits of professionalism from an old colleague who wasn't the best instrumentalist, but by god, I secretly respected him the most because he knew how to do these things. The general public did too 
Of course those aspects are nice for a video recording. That doesn't mean musical points, minor as they might be to you, don't have merit discussing. (BTW, I did enjoy your recording.) There's no reason to take offense if someone finds some slight detail they think you could improve on.
The Bach subject doesn't split off into two, it just sits there in a voice above or below (only Busoni's doublings later on makes it more interesting).
Plus, this isn't what I like about musicians in general, is that this Scarlatti statement even though eloquently written, is all rhetoric. It's overly subjective and over-romantacising of what it simply is, a pedal tone. It's almost validating an overly simplistic musical tool which I remember finding much of Scarlatti's music as. If you pull a rather high level Schenker analysis on the bach subject (just like a mini-step reduction), you'll see the pedal tone reduced down to a elongated whole note rather quickly with the d-minor in eighths or quarter's depending on which beat you choose to reduce.
I think you are compounding [simplicity versus interest] with importance/structural coherence.
They don't correlate at all (There is actually a natural opposition between the two.), the art of music is the appropriate balance between both. There's a certain level of simplicity needed to make music more comprehensible to a listener, but it also needs to be complex enough to maintain interest. This problem underlies the very essence of music at all levels. [And yes, the implication here is that the aural sophistication of the listener does indeed have a role.]
It's a simple device, but the pedal tone provides an important structural line that clarifies the underlying tonal structure of the piece.
Reduction doesn't mean elimination just because it further recedes into the background.
And I think you might slightly be missing the point of Schenkerian notation if you think that means having a longer note dismisses the role of that "pedal note". By virtue of having, a longer note value, it has more structural weight. It's more important to the underlying tonal structure that ties everything together, and has more conceptual priority. It becomes a tonal reference point for the other pitches.
The composer already did part of the work for you by rearticulating it in the music. Repetition is an operation that confirms conceptual priority. It's your job to figure out the right balance, and you can argue the degree to which it should be heard.
You want to clarify the actual, interesting moving line that provides interest; however, you don't do it at the expense of eliminating a background structure completely. It needs to be a continuous drone in the background. Subtle, but there.
TLDR
It's not as interesting to the listener, but it's more structurally important and provides tonal context for everything else.
Balancing it appropriately is not the same thing as eliminating it completely so that it's not audible on a recording at all.