It is not possible to filter-select microtonally inflected pitches when using a custom Tonality System. I don’t know if there’s a plan to make this work in the future, along with transposing functions and Shift-I which likewise don’t work, or work poorly, in custom Tonality Systems.
But I have a suggestion that would be quite useful, perhaps also for standard notation, and does not seem difficult to implement. In addition to “select E flat”, “select E natural” etc. there could be an option “select all the E’s, whether chromatically altered or not”. So, when in the G clef, all the notes on the first staff line would be selected, whatever the accidentals. This selection would work for any microtonally altered notes.