I bought a JCW strut brace from a vendor online. The photo below shows how the JCW strut brace mounting brackets are aligned with the bolts on the suspension dome. There is supposed to be an indent/cutout where there is a bolt underneath. Currently the mounting brackets do not sit flush on the dome. Has anyone else had this problem? And can this problem be solved by just removing the small bolt underneath?

I just got the brace too, only my cutouts for the bolt are on the back side of the brace (so they actually go aroung it). From your picture it looks like the mounting points have been installed on the wrong ends of the brace or else the whole brace is on backwards.

If that's not the case, then yes you can remove the small bolt that is underneath. It is actually a camber locking pin. Some people remove theirs as it allows you to adjust for more negative camber (better for autocross).

Installation instructions: http://www.minimania.com/pdfile/R56_JCW_Strut_Brace.pdf