It certainly is a logical question.
However, keep in mind that what you’re making through this process is a profiling target that will be printed on your printer. Therefore, all the colors on the target that get printed out will necessarily be in the color space of the printer anyway. We’re trying to sample similar colors to the ones that you’re having trouble with; it does not have to be perfect, we just need something that is nearby, to give the profiling software more information about that color area so it can do a more complete job. Even though the existing profile is not perfect, it will be good enough for this purpose (unless you have a really bad printer profile, and in that case you should probably start all over!)
If you are really concerned about this, then take it as an iterative process. Convert the image to the profile, sample the offending colors, make a new target, create a new profile, test it by printing with it. If it’s still bad, convert the image to the new profile, and sample the colors again, etc…