Hmmm... so maybe it's not a bad idea in general..... but it had better be well thought out and executed.
To eliminate the center pin slop and extend the distance between refrence points, maybe 2 pin locations would be a better option. That would let you have them ~3 inches apart and have a ream-tight fit at both points.
BUT... maybe an even better option is to make a jig (Maybe magnetic?) that would let you dial it in accurately. I've seen something similar to what I am thinking of for table saw fences.
http://www.rockler.com/product.cfm?page=16755
The problem I've always had with adjusting stuff like this is the "bump and test" method... I just never seem to be able to get it really balls on. With an add on jig I could dial it in then lock it down and maybe indexing wouldn't be such a hassle. Made general enough it could be handy for dialing in all kinds of things!
I also just got a set of DTI and mics at a local auction, I need to get familiar with them. Random question on magnetic bases... how tight do they hold on? Just using a regular 1" dial indicator I often found the base to be moving instead of the DI... I finally gave up on the one that came with it and swapped out a hard drive magnet. It has it's own issues, but once it's on, it's on baby!