This is actually a pretty common question. Another form of this question that we are commonly asked is how do I get the right concentrations when using a very minor isotope of Ca such as Ca43, which only makes up 0.13% of calcium? You can insert whatever element you like, I just picked Ca because it's a fairly common internal standard.
The answer is that as long as you're measuring the same isotope in your reference materials (RMs) and your samples, and there is no large isotopic difference between the two, the isotopic abundance cancels out. That is, using Ca as an example again, if you're only measuring 0.13% of the calcium in your RM, and you're only measuring 0.13% of the calcium in your sample, it all works out.
If there is a large isotopic difference between your RM and your sample, you get situations as discussed here.
If I haven't answered your question, please just let me know.