Mixing and mastering are traditionally seen as two different stages of the production process. Putting a "mastering plugin" on the stereo out of your mix is not really "mastering", it's maybe a sort of "quick mastering".

So, it's a common practice to first mix and then bounce to a stereo file. Then you master the stereo file (= your mix) very carefully listening and making small adjustments to improve and optimize the overall sound! If you can you can also delegate the mastering to a dedicated mastering engineer, who listens to your mix with experienced and neutral ears and makes the necessary adjustments.

Of course with modern computing power you can do both in one session, but then you will run into those issues you describe, where when changing anything in the mix, you will also have to readjust the settings on the master buss (stereo output). So it's imho best practice to seperate mixing and mastering.