It's best to keep them as a matched set to preserve sound quality as sound pans from speaker to speaker. This my sound off but it could be your sub that is not setup properly that makes you think that the center is not sounding good!
Rainbow effect is inherent in single chip DLP projectors, the best single chips I've seen are Ronco projectors! Your room dimensions are pretty even (problem) and you can't move your sofa, so you'll probably need some bass traps and maybe a BFD to get a decent flat response up against the back...
We have similar shaped rooms and you will find that moving the sofa away from the rear wall will improve the lower registers, and provide a better location to mount surrounds as well. You did not provide your room dimensions. One of the most important criteria for speakers in a home theatre is...
The best recommendation I can make is to build another front for the centre, odd as it may seem. What the other posters are alluding to is the ideal of having "all" your speakers the same "voice" for LCR and surrounds! That way as the sound pans from speaker to speaker it will sound the same.
To the OP, if you're just setting equal levels then the accuracy between the digital an analog meter is not that important, once all speaker outputs match. But if you need to know accurate numbers any meter you use will have to be calibrated.
Don't jump off the deep end, raise your shields or load your photon torpedoes just yet Phaseshift. It was a straight forward inquiry not intended to start a flame war. As a user of REW, my questions were for educational and informational purposes and to gain insight into were or what was...
Phaseshift,...would you mind elaborating on your REW findings, as to what setup was used for the comparison, i.e. mic/s, computer & OS and .cal files etc?