I didn't actually mean for you to use the dof preview every time you set the lens at an intermediate point between the detents- it was only a way for you to see right now that the aperture does change continuously as you rotate the ring rather than in a series of jumps. Frankly it gets a bit boring watching apertures closing down after the first couple of times. I don't know why your handbook indicates not to alter aperture whilst using dof preview, though I can guess. I don't think they want people systematically zooming up and down the entire aperture range to see what happens to dof as part of their focus routine for every shot. I think they'll see that as a recipe for early wear-out of the mechanism in the lens. Doubt whether it will do any harm to do it a few times though, as indeed I have clearly done.
You shouldn't use the dof whilst metering with the AE11 prism, otherwise it will as pointed out cause an inaccurate reading. This is not the same as saying that you shouldn't use the dof preview with the metered prism fitted- you can check and adjust your focus using the dof if/when appropriate before or after you meter.
There is little point trying to use or set apertures between the full stop detents if you are using the AE11 prism E on auto mode. That's because the prism can vary the shutter speed down to a third stop - so you don't need that flexibility on the aperture. It won't of course tell you exactly what shutter speed it's really using - it will simply indicate the nearest full stop.
Will the AE11 prism take into account any half stop aperture settings? I don't know and my Hove guide isn't saying, but this prism was introduced way before there were lenses with half stop detents ( introduced in 1992) so they'd have had to be pretty far-sighted or maybe just lucky. Its not simple to work it out either- because if you start at f11 and then move the aperture half way to f16 you either won't get a change in reading (inconclusive) or if you do well it could be because the prism thinks you're now on f16.