If 3:00 and 9:00 really are both negative, that would indicate that the opening is out of round.
If you take a known round hole that is "perfectly" concentric with an axis (crankshaft) and instead of using "zero", you set the indicator to +.007 and rotate it, all 4 locations should read +.007.
That shows that the hole is round and also concentric to the crankshaft. Normally you set it at 0 and hope they are all 0, but if you use +.007, then you hope all are +.007
If you set it at +.007 at the 3 oclock position and it reads +.007 at 3,6,9 but NOT at 12, that indicates that the hole is out of round but basically concentric
If you set it at +007 at the 3 oclock position and the hole is round, then a -.007 (minus) reading at 9 oclock indicates the hole is not concentric.
The thing is that someone checking a bellhousing should first verify that the hole is round. Probably going to find some minor .001/.002 variation, but need to know for sure it is reasonably round before proceeding to check concentricity.
Simply saying that if 3:00 and 9:00 are both negative isn't completely correct. If the hole is round, a -.007 at both locations indicates that it IS concentric. If the hole is not round, it is possible to get a -.007 at both locations and also NOT be concentric. It would just depend on how much the hole is out of round.
When indicating parts in on a milling machine so that they are centered under the chuck, you simply look at the indicator between the 3 and 9 readings and move the part to zero. The indicator will have a plus in one direction and a minus in the other. As you move closer to zero, the plus and minus readings will get smaller. When you are close, you change to the 6 and 9 locations and do the same thing again. Then usually there is a little more adjusting and indicating a second time to get it perfect.......but you have to have a round hole to begin with.