All three of those airfields are busy. But following the recommendations that GA request transit through MATZs it seems odd that you have been forced off your route after you've had your transit approved.
Much of MATZ crossing approvals is dependent on the height you wish to/can fly at. In general they wont want you below the radar circuit, and with the high ground to the West I'd suggest that a touch over 3000' would be preferable and therefore no reason for a MATZ transit as you'd be above the bloody thing and above any inbound traffic.
My thoughts on your experiences are that there has been a breakdown in comms between Linton and Leeming. Meaning that although Linton approved your transit, Leeming were unaware of your track until handover. Linton is a separate piece of airspace after all. This would put you and any Leeming inbound traffic in confliction. Although I find it very difficult to believe that the units in question do not speak to each other every second due to proximity. But it's possible, especially with fully trained yet inexperienced controllers and pilots at the same place. From the North Leeming would have more time to plan and co-ordinate your transit hence fewer cock ups.
The only other consideration is that during your transit recovering sorties popped up out of low level unexpectedly and you would be required to make way. This isn't unusual, and aircraft based at the airfield will take priority over everything other than emergencies. It could be coincidence that it happened twice, but unlikely imo.
The most worrying thing is that you were pointed at DTV and then sent en-route! If you were already within Durham's zone panic may have set in at Leeming as they shouldn't be able to control anything in Durham's airspace; if you're not on his frequency you are not his problem. The bosses at Durham may have had words.
Personally I'd try and fly above the MATZs, or not bother talking to them at all. Playing by the rules it's only mandatory to remain clear of the ATZs, if it's not the most mature approach to such a situation.
Good luck next time!
GW