When using the same feature tag for substitution and feature variations, the substation is not applied when font variations are used.
Test font: TestVirtualMasterAlternateLayer.glyphs (3.3 KB)
This uses rclt for a substitution and sets Feature for Feature Variations custom parameter to rclt. Setting TEST axis to any value will break the variation. It seems that the FeatureTableSubstitution uses a feature with only one lookup (that one that substitutes the alternate layer), and the existing lookup is omitted.
