When you said low on oil did you mean it was about 2 qts low, or only had 2 qts. (which would be 5-6 qts low)

If you were just 2 qts low I wouldn't expect any engine damage. If the sound is from the engine itself I'd pull the oil filter cap off and see if it is all together properly and if it was holding oil properly etc. I've heard of cases where a non return valve comes apart and gets stuch in the oil filter housing. So check in there for any foreign parts/materials and for any signs of metal in the oil.

It doesn't sound like valvetrain noise, but sounds like it is either from the lower rotating assembly or possible the flywheel area. And since it goes away considerably when in gear there is hope that it is in the flywheel area, but it may still be in the crank/rods etc. Did you have any transmission work done recently?

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