It probably varies by airline but, on UA, UA fares often don't price at the MR rate unless the starting city is the listed one but if you tack an extra segment on the end, it prices at the MR rate plus the one way.

For example, I'm positioning from DFW and I had to book my LAX-BAH run as DFW-LAX on one ticket and LAX-BAH-LAX-DFW on another for it to price the LAX-BAH-LAX at the low MR rate.

I agree about allowing extra time for connection from your positioning flight and I would also use the same carrier as the main MR to have a better argument in case of a positioning delay. I'd rather talk about my UA flight being delayed before a UA run than have to beg for UA mercy when my WN flight is late.