Agree on many things...
My guess is that #4 of Secret Wars will tell us that the Beyonders are controlling Doom...
No way Doom had the power to win a battle against the Beyonders... And Issue #5 has a note that say: Owen Reece died for our sins...
So, MM must have died to start the final incursion and the Beyonders must had take possession of Doom mind and create this Battleworld to their experiences...
Additionally, when wasn't "Secret Wars" a project from Beyonder(s)?
If this was all a "project" from Doom, this wouldn't be called Secret Wars...
It would be called "House of Doom" or something like that