The kit I have at home is an Arbiter flatlites kit - the kick and three toms only have one side ! I've always miked the toms from beneath because my clips wouldn't fit on the rims. But I love the sound they yield.It's not unheard of for folks to remove the resonant head from their toms and mic from underneath, or even to leave the head on and mic from underneath...
Moral of the story: Put the mics where they capture the sound you're looking to capture.
If it SOUNDS right, it IS right.