It depends on how I fold them. I can make them feel the same by changing more than which thumb is on top.
If you interlace your fingers, the index finger that is on top is the same as the thumb that should be on top. (if you continued the pattern the opposite thumb would be next)
If you fold them like the pic of Reggie, the more closed hand's thumb should be on top. (the angle that the thumb comes in at is a little different between the open and closed hand)
The discomfort comes from just switching your thumbs. Switch the layout of your hands and you may find that the other thumb being on top may be comfortable as well.
My left thumb is the that ends up on top when I subconsciously fold them, but I can make the other thumb work as well by switching how my hands are laid-out.