Is there any advantage or disadvantage to this method verses simply stacking all the individual calibrated sub frames together (not the masters)?
If you stack just all the subframes together, you will not be able to reject hot pixels, satellite trails etc. as efficiently. Crudely explained the rejection algorithms assume that the subframes are very similar on average. That's why the outlier values are easy to spot and reject. Subframes taken with varying filters are not similar at all, so the rejection fails.