Bare shaft tuning or any other tuning has absolutely nothig to do with a bows center shot. A bow has a dead center spot and that's it, period.

Now when you indtroduce the human factor to the bow, the place, left or right of center, that you get the best tune will almost always change. This is because every person holds and anchors differently and almost no one holds a bow perfectly straight. We all torque the bow to some degree. However, the bows center shot position has not changed. It is and always be in the same place. You just have to determine how far left or right of that spot that you shoot the best.

Bare shaft tuning comes after you set center shot to get a starting point.

The tool that you describe that attaches to the limb bolts is definetly not the best tool to use if you want to find the absolute dead center position. AS you stated originally the cams are not center of the limbs.

Easy Eyes (same people that make the arow wraps) makes a laser that you attach to your riser. Line up the laser with the string at the nock and then twist it to align the laserwith the tip of your arrow. This is the most accurate tool made for finding center shot but it will cost you.

Golden Key makes a simple but effective tool called the TRU CENTER GAUGE.