From what i've gathered reading the manual and using the machine, yes, the wheel can be good (the measured runout will be ok) but the tire can be bad, or vice versa, but the machine cannot get a very accurate reading of the roadforce on the tire if the wheel has too much variation (though i think it does take this into account when doing the matching process). The machine can and does tell you whether the tire or the wheel is causing the assembly to be out of tolerance, or at least the way our is setup it does.
If after the balance the machine detects excessive variation, it will ask you to re-measure the rim runout using the dataset arms; using the correct location of the arms against the wheels is crucial to obtaining correct data. Some rims cannot be measured on both sides very well, and it's not very convinient to dismount the tire to measure a bare rim.
I belive the machine does take into account rim runout and tire roadforce variation when calculating the assembly's total variation in pounds. However, rim runout (which the machine converts to pounds through some formula) i think has different tolerances than tires. There are three settings for tires, P, P/SUV, LT/SUV and you can make you own as well, and modify the tolernaces for the presets. I am pretty sure I remember there is a way to change the rim runout tolerance for the wheel as well.
I remeber when using the roadforce measurement screen, when you make the marks, it can tell you in pounds, how much force is at the point you marked either on the tire or on the wheel. When you are on the balance screen, it tells you the pounds on the total assembly.
As far as changing the tolerances, the manual gives pretty good instructions on how to do so. if you can find what "K" button it is, i think the onscreen prompts are good too. I've never changed the default tolerances.
When I measure the rim runout using the dataset arms, the machine tells you either pass, fail, marginal from what i recall. You can also hit one of the "K" buttons to show the actual readings on the runout. Same goes for the roadforce variation on the tire; there is a "K" button you can push to show a graph and numbers of the roadforce on the tire, and also the assembly as a whole.