The last time I used Av mode for a I had hoped that by simply adjusting the exposure in ACR to compensate for the differences in capture exposure that I could even out the sky. Unfortunately, that didn't work, which made me wonder about the possible effect of exposure on color/tonality (yes, I took the shots in rapid succession; yes, I synchronized the WB on the RAW files; and no, I didn't use a polarizer). Can anyone think of other variables to consider with regard to this issue?
This is not a simple issue.
First think of the reason you shoot with variable exposure. Typical scenery: as you turn, the camera is turning into or away from the sun; the ideal exposure changes gradually. A given exposure will blow one frame, while another one gets underexposed. So, you shoot it with variable exposure, then in PP you want to equalize the frames. This means, that you pick one, perhaps the one with a medium exposure, and adjust the neighbouring frames to this one. Thus in effect you reverse the result of the variable exposure. Now go to the next frame and do this; the adjustment has to be much more. So, you end up with a set of frames, which look exactly (in ideal case) like you would have shot them with fixed exposure.
I that, what you wanted? Most probably not. Though this can help on noise issues, that's not all. You want to lighten those frames, which would be too dark with the fixed exposure and/or darken those, which would have been overexposed.
In effect, you want to adjust the overall intensity over all frames continuously. This requires the adjustment of the frames pre- or post stitching (but before blending), gradually. You need a graduated mask for the adjustment, "bridging" over the frame, "connecting" the two adjacent frames. This is, what I ment with "extraordinary effort".
Another, cheaper way is to adjust the frames for example in ACR not with "exposure" adjustment but with fill light, recovery and/or brightness. You can match the sky (more or less) this way, and ignore for example a landscape, for it is not as sensitive to differences as the sky. (Note: a water surface is almost as sensitive as the sky). However, now the colors of the frames will go apart; only the grey remains grey.