Based on a request from Brian Searle, I have reviewed the code for File > Export > Spectral Library and found:
1. It always exports the first spectrum (chrom info) for a precursor instead of the "best"
2. The way Skyline currently calculates the "best" has not been updated since we moved from LegacyScore
3. There is UI code in the Model class for doing the export which needs to be moved to a UI folder

For 1, we should change the code to be something like this:
            SpectrumMzInfo spectrumMzInfo;
            var isBest = replicateIndex == nodePep.BestResult;
            if (!spectra.TryGetValue(key, out spectrumMzInfo) || isBest)
            {
                spectrumMzInfo = new SpectrumMzInfo
                {
                    SourceFile = DocumentFilePath,
                    Key = key,
                    PrecursorMz = nodeTranGroup.PrecursorMz,
                    SpectrumPeaks = new SpectrumPeaksInfo(mi.ToArray()),
                    RetentionTimes = spectrumMzInfo?.RetentionTimes ?? new List<SpectrumMzInfo.IonMobilityAndRT>(),
                    IonMobility = im,
                    Protein = nodePepGroup.Name,
                    RetentionTime = rt
                };
                spectra[key] = spectrumMzInfo;
            }
            spectrumMzInfo.RetentionTimes.Add(new SpectrumMzInfo.IonMobilityAndRT(chromFileName, im, rt, isBest));

For 2, we need to improve PeptideDocNode.CalcBestResult() to use the mProphet calculated ZScore when it is present, use the full DefaultScoringModel if not, and use maximum precursor score, not summed.