Bottom mounting is definitely preferable.
I bottom mounted my Wicos by routing a 3/8" recess for them.
That is in a narrow module, and I have had no problems with it at all.
The option that will give you the maximum stick height without bolts screaming "top-mount" is to recess the bases from the top enough to hide the bolt heads, and then fill in the rest of the recess with wood, to bring it back up level with the top of the CP.
The problem with this method is that, if you ever want to change them, you have to tear your CP apart to get them back out.
It does give you the highest stick though, so you need to decide what is most important to you.