I have the same problem with the Atlas #6 Custom Line turnouts. I have a triangle sided, fine file that I use to file down the frog.
I sit the turnout on my bench use my left hand to hold the turnout in place. I use my thumb and first finger to guide the end of the file straight while I use my right hand to run the file back and forth.
Using the triangel type file gives you something to grip while still pushing pressure down and sliding the file back and forth.
I file until it just touches the other rails checking by sliding my fingernail at the ends of the frog. Continue until you fingernail slides over without catching.
Bill
Are you sure it is the frog rail height and not the higher than ideal fill in that frog? It would be a shame to wear away the rail heights only to find that you have not solved your problem because it was the filler all along.
But, yes, you can use a suitable stone on a Dremel-like tool. It would take some considerable care and skill to keep a mill file flat and level while you buffed the frog with it by hand and still not do unwanted things to the rails nearby.
Once I determined what's what, I would use a Dremel and do several slowish sweeps, running the same engine and cars through it until it seemed to work.