Is there any reason to get the 3-9 as opposed to 3-12 other than a $20 price difference?

No thoughts on the difference between the 2

For the BDC reticle to work properly you need to be at the highest magnification.  What high magnification do you want, 12 or 9?  Are you hunting with it?  If so too much magnification is definitely possible to have happen.

The 12 at highest magnification will have a smaller exit pupil, this may cause it to appear to be dimmer at full power in low light conditions, do you plan on hunting with it in those conditions?

Probably not.  I usually blow prairie dogs up in the day time.  But I never thought about the light transmission.  Thank you