Yes strictly speaking it's a different computation, but the differences are so small that it won't meaningfully affect the outcome of Shor's algorithm.

One of the most important things to realize when optimizing quantum algorithms is this: approximations are overpowered. The difference between 99.99999% accurate and 100% accurate can be a factor of 10 in cost. And there's lots of places where a 90% accurate algorithm is more than good enough.