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4050 (or TLM102) close about 2 feet out and ORTF mc012 about 5 feet out?
Will this result in more phase issues (comb filtering, image shifts, etc)
It will sound fine. That kind of thing is not really an issue in a venue like a church. Phase has more to do with wavelength than the BS 3 to 1 rule that has been crammed down every beginning engineer's throats. A guitar's frequency range is really too high for phase to be a problem at that distance. Though I would suggest maybe 6+ feet away with the stereo pair in a NOS pattern, which I think is better than ORTF for solo instruments, and two spots on the guitar in different positions, balanced to taste. You'll find with classical guitar, 80% of the sound is going to come from the stereo pair, and spots are used just for a little added presence.
That said, the spots + room should work nice. I did a lot of recording in a church (well, it was actually a gymnasium, but they did a nice job on the acoustics! They called it a santuarium :P ) with spots on the stage then an ORTF of old NT5's up against the back wall. Those NT5's always had an amazinly nice reverb in them.