I would remove the top,because if you remove the bottom,and you fill it with ATF it will have a chance to leak out the bottom.

Im going to tell you this,if you do this at home,it will smok eup your neighborhood
I started my car at night,when I did it,and the smoke went about 5 houses down,on both sides of mine.

No it wont mess up the internals.BUT you will foul the plugs..
The longer the ATF sits in the car,the more it breaks down.But anything after 4-5 days is a waste.

An old piston trick is to put atf in the oil,quiets the lifters.Breaks down carbon