Hopefully not, because I bought one of those, too. I remember reading that some of the covers interfere, and some don't. Supposedly, the Ford Racing cover is compatible with the MM stuff, but hopefully someone who actually has all of these components will chime in.
I had the same cover on my 98 GT with the MM PHB and it was close but it cleared. The newer low profile ones clear no issues. When i talked to the owner of MM at a track day he said they put the warning there because on a case by case basis it may not fit.