I think the change in sound you're hearing is because the pickups are dropped so low, per the picture. The pickups already look pretty low and you have the additional spacing from the wood cover on the pickup.
As the pickups get farther from the strings, there will be less bass and less attack, which may account for the acoustic-like tone. If you have another Strat, try cranking the pickups all the way down and you'll probably hear some similar stuff going on.
With all other things equal, you probably won't hear the difference between pickguard materials as they're relatively tightly attached to the body. There will be an effect from the mass of the pickguard (a 70's brass pickguard will be a lot heavier). A steel pickguard would change the tone because is distorts the magnetic field. The big bridge plate on a Tele is doing this and is very obvious if you switch to a brass Tele bridge (the way it sounds explains why you almost never see brass Tele bridges, and makes me wonder if there should be a steel plate for Strats).
The reason normal Strats are so sensitive to pickup height is that stock pickups use magnetic polepieces which are so powerful that they damp the vibration of the string if they're too close or can even cause false harmonics.
Although the pickups being mounted to the body cause them to be moving when sensing the strings, I think that effect is very minimal as well. When you're playing a note on a guitar, the motion of the body vs. strings should be proportional to the ratio of the string mass vs. guitar mass. That's a big ratio, so it's probably a pretty small effect relative to the circus of other stuff that's going on when you hit a note.
This ratio can change with the weight of the instrument, but there's a much bigger effect there, as the string motion is affected as the body accelerates up to the pitch of the string. You'll hear this as a big difference in attack between a heavy guitar and a light one, but this is somewhat separate from pickup motion.
Mica often points out that neck woods dominate the sound of Alembics to a greater extent than on other instruments because of the neck-thru construction. Both ends of the vibrating string are sitting on the same piece of wood and the laminated neck is engineered to give better stiffness and consistency than a neck made of a single piece of wood, which may or may not be good.
As you mention (and I think I did in the past), the guitar is a big mechanical filter with many variables, which include mass, stiffness, resonance, etc. If you want to have pure string vibration, then having a stiff, uniform neck is the best way to achieve that. If you make the neck of one wood and the body of a different wood, the pure vibration of the string is disturbed where the materials interface. This is a physical impedance mismatch. This is often illustrated in an introductory Physics class when they ask you to look at the wave motion of a rope tied to a doorknob and then change from a uniform rope to a thick rope attached to a thin one. The non-uniform rope will try to set up different resonant frequencies in the different parts and, depending on how well those frequencies get along, you may not be able to set up a steady motion. That's the difference between a good Strat and it's bad brother hanging right next to it at your local guitar store - even if they were build one after the other in the factory, each piece of wood is different and affects the attack, sustain, and tone of the guitar. Having a through-body design gives you the best chance of preserving the natural string motion, particularly the fundamental.
The cavities in the body will have the effect of changing the body mass, but in an Alembic the effect is reduced because of the thru-neck. Even though the caps are thick, I do think a Series bass is much louder acoustically than a solid body bass, but don't really hear that in the amplified tone.
David Fung
