Alignment with 2 tooling balls only

Don is 100% on this.
If that plate is parallel to the CMM Z axis in both X and Y directions, or if you are supposed to measure a plane on it for aligning, cool, otherwise no go.

To your other question, sure.

If for some reason engineering is aware of, one of those tooling balls is zero, or the mid point between them, whatever, then you could easily have nothing on your part that is zero. This would matter if you were inspecting assembly dimensions. I've never been asked to do this in the way you are suggesting, but it CAN happen.
And with your wording, they gave you a report. I don't write reports that output the features used to zero the part for their location, so I have nothing at X0 with zero deviation. maybe they just didn't output whatever is zero.
Neither tooling ball being zero, and them having different deviations from nominal strikes me as odd, but it could have some weighted offset for some reason, I guess. They made the tool, put the "Gold Standard" in it, measured the balls, and that's what they want the error on the balls to be from that gold standard.

Why are you doing this? Customer sent it to you? Supplier sent it to you and they have design authority? Shipping brought it to you because someone told your sales people you need to use it?

I'd point out that two balls don't work alone, and ask what you are missing from the people that supplied the tool, or from their inspection.
I'd decide if they had the authority to tell me how to inspect the part.
I'd decide if I believed that what I was being told was sufficient not to kill or maim someone, and not to cause my employer undue liability for product and/or recall.
All three check out, go with it.
One doesn't check out, express why you are concerned (safety) and what gives you concern (nothing is actually zero on the part so where did XYZIJK come from?) and see if someone can allay that.

If the design authority sent it because they've been using it and making parts for two decades with zero loss of property or life, that carries some weight all on its own. But with the limited information you seem to have been given, I'd have concerns.

Also, someone must already have a program for it (you said there was a report), can they give it to you? A printout of it if it is a different manufacturer's software? Why are you re-inventing the wheel on this. Looks like someone put some money into that tool, they must have had a concept for it's use.

Don is 100% on this.
If that plate is parallel to the CMM Z axis in both X and Y directions, or if you are supposed to measure a plane on it for aligning, cool, otherwise no go.

To your other question, sure.

If for some reason engineering is aware of, one of those tooling balls is zero, or the mid point between them, whatever, then you could easily have nothing on your part that is zero. This would matter if you were inspecting assembly dimensions. I've never been asked to do this in the way you are suggesting, but it CAN happen.
And with your wording, they gave you a report. I don't write reports that output the features used to zero the part for their location, so I have nothing at X0 with zero deviation. maybe they just didn't output whatever is zero.
Neither tooling ball being zero, and them having different deviations from nominal strikes me as odd, but it could have some weighted offset for some reason, I guess. They made the tool, put the "Gold Standard" in it, measured the balls, and that's what they want the error on the balls to be from that gold standard.

Why are you doing this? Customer sent it to you? Supplier sent it to you and they have design authority? Shipping brought it to you because someone told your sales people you need to use it?

I'd point out that two balls don't work alone, and ask what you are missing from the people that supplied the tool, or from their inspection.
I'd decide if they had the authority to tell me how to inspect the part.
I'd decide if I believed that what I was being told was sufficient not to kill or maim someone, and not to cause my employer undue liability for product and/or recall.
All three check out, go with it.
One doesn't check out, express why you are concerned (safety) and what gives you concern (nothing is actually zero on the part so where did XYZIJK come from?) and see if someone can allay that.

If the design authority sent it because they've been using it and making parts for two decades with zero loss of property or life, that carries some weight all on its own. But with the limited information you seem to have been given, I'd have concerns.

Also, someone must already have a program for it (you said there was a report), can they give it to you? A printout of it if it is a different manufacturer's software? Why are you re-inventing the wheel on this. Looks like someone put some money into that tool, they must have had a concept for it's use.