I can't think of any systems where you would get to roll a dice pool that looked like, say (1d10+5, 1d10+2 and 1d10+9) and keep the highest let alone a pool like (1d6+1, 1d10+4, 1d20+5).
I think its kind of an edge case and its most likely to happen because people (me..) go 'oh i need to roll a d20 and there is a mod on the dice so +5 and oh i have to keep the highest' instead of 'i need to roll a set of dice, where i keep the highest, and the dice look like this'
Should just be as easy as saying 'if you want to use X style, use Y order'. I think the only problem comes because the error is sort of arcane to the uninitiated. As you can tell I did figure it out by just going 'oh well what if i put the mod last' but you know what they say about trusting the end user.