There are a great many applications out there that do not kern or do not support any of the open type features. Some do nothing more than a very basic rendering of the text.
I thought about adding ligatures to substitute for proper kerning but the problem is that the applications which don’t kern are generally the ones that don’t do ligatures either. 
But in general applications where the function of the program is to present text properly rendered (word processors & desktop publishing) do have better support for open type features. I don’t know about e-book compilers. One would have thought that they would do their job properly but there are no guarantees.
As Bhikkhu Pesala said including a Legacy Kern table is probably your best option at this point, it will make the font bigger but older applications are more likely to support that type of kerning if they support kerning at all. Microsoft Word until very recently only did kerning if the font had a legacy kern table.