In the FDK, the features are in the order you put them in the feature file.
InDesign doesn't need the features in a specific order. However, it is true that it will process features in the order they're in the font. So, let's say you have 'liga' ahead of 'smcp', and the user applies both features. They could get the fi glyph, and then the smcp feature isn't set up to process the fi as input, so you can end up with a word like "OFfiCIAL" in small caps.
However, it is likely that in the future, Microsoft's approach will be to process features in a specific order, regardless of the order in the font.
So, basically you should both order features and set the inputs such that when multiple features are applied, the user gets the results you want and they expect.
Regards,
T