I know what you mean about those self centering bits. There is too much play in many of them to be accurate. Personally, I think installing metal hinges depends on a number of things:
1) An accurately cut mortise.
2) Using a quality hinge (Brusso hinges for example). There shouldn't be any play in the hinge and it should be stiff, not sloppy. You do get what you pay for when it comes to hinges.
3) Then with the hinge seated in the mortise, I mark the center of one hole with an awl. I trust my eye to find the center.
4) Set the pilot drill in the hole, ensure you're vertical, and drill to depth.
5) Install the other hinge in the same manner and then fit them to the lid with a single screw.
6) Ensure the lid lines up and operates smoothly and all being well, mark and drill the remaining screw holes then fit the screws.
7) If you really want a high-end craftsman finish to your hinge installation, you can go the extra mile and fit the screws so that the slots all end up in alignment when tightened. There are a number of ways to do that which involve either tweaking the countersinking on some of the hinge holes to allow the screw to turn slightly more as it becomes tight. Or, you can carefully file the underside of the screw head to achieve the same result. This might be a step too far for most people though.
I'm sure some of the great box makers on LJs will chime in with some great tips.