I'd always distinguish between the optometrist (the eye exam guy) and the dispenser (the person who dispenses the glasses). The latter shoudl do as you wish or you should go elsewhere especially when you have a well defined need (there are lots of folks out there with "odd needs": pilots (overhead instruments to read), golfers (just enough).
In fact the latter one (if you can find anyone making the lenses might be an option for those that make simple field notes.
Another alternative is a voice recorder for field notes.
The usual alignment for bifocals is the line should be at the level of the lower lid.
I've used quite a few online glasses makers (including Zenni). They vary a bit in quality and they occasionally screw up (one example (not Zenni) they left off AR coatings that were requested ... twice

). Some are better than others. And there are others that just "labs" i.e. they glaze your frames with lenses of your choice (they often have a wide range of lens choices from generic up to Nikon and Zeiss). They're more expensive than the bottom feeders but I suspect they might have higher quality.
I've also tried tweaking my prescription. The last exam I had for some reason even after a remeasurement (with a slightly changed prescription) and change of lenses was clearly off in astigmatism by several degrees. Tweaking the prescription proved this too. Still not sure what caused this perhaps a head tilt when making the measurements. I'll be going elsewhere for the next exam especially as this same OD has given inconsistent results with that eye over the past decade (there could be other higher order astigmatism issues confounding that eye too). Ideally I'd like to find an OD that can still use a phoropter (you know the old hardware that looks like a gigantic set of SciFi glasses with individual lenses rather than a computer controlled optical system) and then verify the prescription with a trial frame.
http://en.wikipedia.org/wiki/Phoropter
Single vision is easy to make (or rather difficult to screw up!) and the CR39 lens blanks are well under $1 a piece so they're cheap. Bifocals rather more challenge (e.g. to get the same segment height and tilt in both). Progressives really need a fitting (or an experienced user -- it's not rocket science) and a quality maker to make the bins. Unfortunately most don't leave the makers temporary "fitting circle" (which should be centered in the pupil) on their progressives when they send them to the user. A dispenser would fit the glasses then remove those marks. Fitting without them is a bit of a pain in the butt.
But I think the average bin geek here can figure this stuff out. And glases wearers should obsess about this stuff as much as we do about our bins.
