I will agree that if I walked with my dragon while gathering that wouldn't exactly be optimal. But then again, walking also doesn't happen very often with that character since flying IS so much faster. So the walk speed on the dragon is largely irrelevant.
With the numbers I have, I don't actually lose 50% of my speed ever... even on the rare occasion where I do have to walk on the dragon. And I do have over 150% increase in carrying capacity with a disk, not 100% (yes this could be different if I cleaned out my inventory but I have other reasons for not doing that which I won't bother going into here) So a 150% increase in gathering capacity with only a 50% decrease in speed gives a good deal more in gathering efficiency since the only real travel issues would be between the nearest storage structure and the resource field. If you pull golems to you for example, you barely have to move at all while you're gathering so running between the spawn and the storage is your only travel.
On recalling, there are very few instances where recalling is the better option over just dragging the resource to the nearest vault or shop. And in that case, I either just don't use a disk or use a travel scroll depending on how much of the resource I need. If I need 10k of something, a disk will be used since it's faster overall, but if a full inventory/pet covers it I probably won't use a disk.
I... don't see how either of these would mean you lose an advantage. In any case when you sprint or use a road, your efficiency goes up since you spend less time traveling between storage and spawns.
I will admit that I have gotten my biped to quite an advanced stage, but it's really not that difficult to get to that 121 speed now that the base run speed has been upped from 50. Really the hardest thing on the list below to get is the t6 necklace since you have to have at least two classes to 100, hunt down the right pieces, and also find (or be) a jeweler with enough skill to craft it.
Base speed = 65
Fleet of Foot (passive gained at 38 Ranger, mastered at 76 Ranger) = +10
Gift of Speed V (requires level 80 and 800 augmentation skill) = +10
Speed crystal (best of the t4 versions/worst of the t5 versions) = +11
Priceless Adamantium Necklace (crafted from broken jewelry pieces, requires 105 rating to equip) = +25
Total = 121
That's where my current gathering setup gets me, speed could go even higher if I used any of the following:
Speed technique on the boots = +12 (The only reason I don't have this on my gathering suits is because I have them triple-teched with other things and speed wasn't a huge priority with how much I get already)
Best possible speed crystal = +2 (total of +13 but here I'm swapping the speed crystal I currently have on the biped with the best)
Quint's Quickstep Potion V = +10
Swift Feet V = +14 for 2 minutes
Spun Sugar (bought at summer festival but is painful to get much of) = +5
(OR NOT AND)
Cotton Candy (bought at summer festival but is painful to get much of) = +10
Maximum without roads/sprinting = 169
So counting only things that are easy to get (fleet of foot, gift of speed, speed boots, quickstep potion, swift feet) you get, oddly enough, 121 speed.