Setting the mains to full range through bass management, and going pure direct will accomplish exactly the same thing - it will send a full range unfiltered signal to the main speakers.

The OP ran Yamaha's auto equalization program, and that will benefit the overall sound of the system even if it is just two channel. If you use pure direct, that equalization will be defeated, and the OP will hear a less refined sound. While the auto EQ is not the best, it is better than nothing at all.

If you are going to use a sub, it is much more simple and easy to use the sub out or LFE out with bass management controlling the crossover point. Running a sub off the pre outs of the L/R mains(and old school two channel mentality) is overly complicated, and not necessary at all. Going this direction causes you to lose the precise high/low pass filters in the receiver which helps subwoofer to main speaker integration. Why make the setup more complicated than necessary, and still not get the best sound?