Tuning shouldn't matter as that's based on tension, intonation is the positions of the nut, frets and saddle.
I'd always intonate when changing strings, it doesn't take too long to do just do it after you stretch and tune them.
One thing though, if you're using alternate tunings for a long period of time check your truss rod and adjust that if necessary you can find some guides on adjusting the truss rod.