Yes, it is rewarding running project at destination sample rate, but in this case, since all stock motherboard cards are clocked at 48khz, running at 44 will give undesirable penalty to processor. And since Logic (i just think guitargod is running logic) is doing all resampling in real time, problem may be even bigger.
But this subject is interesting. Lot of people claim that running at 48 and even higher sample rates do good for many aspects of sound. I must say all of it depends on gear, way of work and music you are doing, just as you pointed out. When working with lots of virtual instruments, personaly I don't see a point running them at high sample rates. But if you are, make shure that sample rate conversion and dithering are the last procesess you will do.
Lots of virtual instruments sound different on different sample rates. Specialy when they are running on samples, since the main rate is almost always 44 or 48k, and if you are running on different rates, there is always unecessary conversions.
And also, it all depends on your gear. If you don't have quality AD/DA and studio monitors, you will never hear much of the sound and little differences on different samplerates...
But main thing is: make music and be happy, don't think too much about technical aspect of it

Cheers