If we do not allow SFX to have any impact on their associated Powers, then we have to expect that either every user of a particular Power is going to be pretty much identical to every other, or else that we have to be very careful during the Power construction to apply just the right Advantages and Limitations to account for every possible future consideration.
Personally, I prefer to just live with the expectation that SFX may have an effect on the effectiveness (or lack thereof) of Powers. It provides a bit of wiggle room that I like; excessive rigidity just isn't as much fun.