Uh, why would that be a problem? Tons of high-end guitars are made up of parts by tons of different brands. Say, it's a Jackson guitar, but it's got a Floyd Rose tremolo (different brand), Seymour Duncan pickups (different brand), Gotoh tuners (different brand), etc. etc. A lot of guitars out there have DiMarzios in the bridge and Seymour Duncans in the neck (or vice versa).
It's pretty common.