So, the good news is: I think you’re overthinking this a little.
When you apply a filter in your DAW, the original audio file is “calculated against” by the filter, however that only applies within the DAW (and the associated project file).
Once you export / render the project to a new audio file (I use Logic, and in there it’s called “bounce”), that new file (mp3, m4a, etc) is just the outcome of the project.