Yes, a well-engineered font should handle the interaction better -- probably the easiest approach would be to ensure that case-substitution subtables are ordere

Yes, a well-engineered font should handle the interaction better -- probably the easiest approach would be to ensure that case-substitution subtables are ordered ahead of ligature subtables. (Though as cobertos noted, the author could have worked around the font issue by more careful use of font variant properties in their CSS.)