I think I see what you're saying. However, I think I am missing something.
One of his big points is that "The wand chooses the wizard"... I mean... "The theory chooses the units" out of convenience. OK. I suppose that might be the case, as I've never sat and worked through an original theory and tried to decide which units were most acceptable. I have worked in natural units in relativity, though, and it does seem to simplify things somewhat.
Going back to the meter stick idea, however, if we rigidly fixed our units, a meter stick = 1 meter, 9 billion-some-odd number of cycles of Cs excitations for time, some particular amount of charge required to exert a force of 1N on an electron from 1 meter (or something similar), and the kg as something similar (I'm having a hard time coming up with an example for mass) - Wouldn't that sort of solve the whole problem of allowing it to be "chosen" instead of us having to determine which of the fundamental "constants" are changing?
Give me a very accurate clock, and a meter stick. I will test to see if c is still equal to 299,792,458 m/s (within experimental error, but let's toss that aside for a second [ba dum])
Measure mass via some good method that I can't come up with right now, check the electron mass.
Give me a meter stick, an accurate clock, and the notion that electron mass is the same, and I can check to see if e is the same. If both of those are the same, but alpha varies, it must be in hbar. With a constant, non varying unit for kg, m, s, and C, you would also be able to check h, if you wanted.
Seeing as how you seem to be more on page with the author than I am, can you explain to me why (in theory) this isn't feasible for determining the constancy (or lack thereof) of "constants"? (I understand the problems with keeping a meter stick in a vault, etc.)
To add:
I'm referring to this comment:
"Hence the dynamics associated with each varying α theory “chooses” the units to be used, on the grounds of convenience, and this choice fixes which combination of e, c and ¯h is assumed to vary."
This seems like a very bad way to do things, in my opinion. "Oh, it's easier to say that e changes, so we'll roll with that."