There's no noticeable loss of accuracy unless you are too close to a gravity source. Don't skip up to 100,000x right after the TMI burn, bring it up slowly, say one click of the "t" key every five or ten seconds, and have OrbitMFD set to Mars reference and start slowing down the Time accel when the G > .2
I use IMFD and make my MCC about halfway to Mars, and only need a second MCC when I get closer if I'll be planning to aerobrake - since that requires a very precise PeA at Mars.