When the reminders come up and I'm taking my break, I'd like to continue 
reading the screen. The micro-reminder comes often enough that it's really 
bugging me to have it in the middle of the screen. My suggestion is that 
WorkRave should let me set where the countdown timer sits on the screen while 
I'm giving my wrist a break!

Really, you should not be reading the screen at all. That's the point of a
break, including micro-breaks. Adding the option you suggested defeats the
purpose of Workrave.

If the micro-reminder comes too often, perhaps it is a good idea to change the
timer settings?