So with the design of the Harris, the depth of the stud shouldn't be super critical. Its suppose to pull the stud into the bipod to adjust tension. It should be fairly forgiving in that retrospect. As long as its tight and not wobbly it should be fine. Use an allen key to tighten down the screw if you don't think hand tight is sufficient.
There will be some flex in everything. Including the stock forend, which I don't think the Magpul stocks have any steel/aluminum backbones that would stiffen the forend. You could also add spacers on the wings of the bipod that come into contact with the stock if you think it isn't on there tight. Or if you helps you sleep at night, get the GG&G mount. Its a $24 mount so it isn't breaking the bank.
I can't think if my Harris has a foam/rubber spacer on the wings to protect the finish on the forend, but the Ebay bipod I have definitely has foam/rubber spacers that would in theory impart more flex into the stock/bipod interface.
Given your current setup, are you experiencing any issues with the way your bipod is currently mounted?