I've never owned a guitar with scalloped frets - and I've never had a problem with clean tapping technique in the upper fret registers. I've played my guitars until a refret wasn't just a necessity, it was mandatory... and still never really had problems.
Take a look at your technique as well as the instrument. Not saying your technique is bad, but I've seen more than my share of self-taught guitarists (or those who didn't take enough lessons to solidify an advanced concept like good two-hand technique) who don't possess good left hand technique/alignment as well as proper right hand technique when using two-handed concepts.
Your more than likely pressing too hard and choking the note since the scallops let you dig a little deeper. Since you said it comes out fine with distortion this is what it sounds like or it could just be an all around sustain issue but i seriously doubt it
At such high frets, whether you have bony or meaty fingers does matter too. My fingers are of the latter type and I have to use the edge of my finger nail at frets above 19-20 or my finger dampens the string and I get choked notes as you describe.