I guess this was originally considered a transitional feature that we ourselves used in ensuring our integrated implementation of mProphet was correct. Great that it has lived on and found new uses, but it is not something we generally focus effort on without a request like this one.
Certainly, we can change the q value column to change non-best peaks to have #N/A, but for now, you can simply make that mental adjustment. The q value only applies to the highest score or lowest p value. It is not possible to assign a q value to the other peaks, because a q value is inherently "about a set of p values", meaning that it is an adjustment to an FDR estimate within a particular set of p values. If we were to assign q values to the entire set p values for all considered peaks, that would produce very different q values than the Detection Q Values you can get in the Skyline reports.
At present, we only output the peaks detected and scored during import, as you have noted. We have never actually done the work to calculate and store even all of the component scores for manually selected peaks. For instance, we never calculate chromatogram-based scores like Shape, Signal to noise, etc. So, we don't actually have them all to export at the time of File > Export > mProphet Features. I always wanted to do this work, so that we could at least assign a Detection Z Score to a manually integrated peak, but we still haven't done it.
The original intent of File > Export > mProphet Features was just to allow normal mProphet testing on the peaks and features Skyline produces during import to ensure our mProphet implementation works like other external implementations. We haven't taken the feature much past that I am afraid, but I am glad it has found new uses.
We will consider your feedback. Switching to #N/A for non-best peaks seems simple enough and if we manage to calculate and store the chromatogram-based features during manual integration (along with othe peak statistics - area, FWHM, etc. - which we currently calculate) then we will consider adding them to the mProphet feature output.
Thanks for taking the time to post your thoughts to the support board.