How can you overfly a MATZ at 3,000 ft when the top of the MATZ is 3,000 ft agl? OK, 3,500 ft alt should take you over the top of most of them, but don't forget, the RAF will want you on their QFE not QNH.
Best to call on the notified frequency and tell them where you are going and at what altitude (not mentioning MATZ penetration) then see what they say; don't forget a MATZ is class G airspace so provided you remain above/outside their ATZ, they can't actually refuse you permission to transit.
As for Danger Areas, don't get confused between Danger Area Activity Information Service (DAAIS) and Danger Area Crossing Service (DACS); DAAIS will tell you if the DA is active then you make your own choice about entering it (although some do have byelaws which specifically prohibit transit and are indicated on CAA charts), whereas DACS will, activity permitting, give you clearance to transit.