The complication arises because some features work together with re-ordering, principally for Indic scripts. Features are processed in batches, and sometimes glyphs are reordered if they result from the operation of a particular feature. Within each batch, the lookups of the features are processed in the order in which their lookup definitions are stored in the font file.
How the reordering and batching are done are in general dependent on the script. Applications have some control on which features are taken account of, though it was noticeable with IE11 (at least, early IE11), that I could not induce IE11 to apply general typographical features to ‘non-standard’ scripts. Firefox, which uses HarfBuzz for rendering, is more accommodating.