I'm on the latest code, but I happen to like hero stacking. I just make it so you need two shots to start a hero mode instead of 1, but I can stack hero's with villains and vice versa. I can confirm that at least with hero stacking on, Danger Room is still linked to beating Magneto Multiball with all hero's started (not completed) like it was in 1.24. Did it yesterday (162M after only getting 5M in Danger Room). Danger Room has also been re-worked in this latest code from 1.24. Only lit shots to start DR are Magneto, and the two orbits (left and right). I drained before I hit all three but I never got it to kick a second ball. Tough deal!!
Now whether hero stacking changes the DR requirement, I cannot say, I love stacking modes so I haven't played any games since it became an option.
On another note, it does seem like the beast shot is glitched during Weapon X multiball. If I get beast running, then start WeaponX multiball, I can't for the life of me complete Beast. Other hero's can be completed during Weapon X (just not started).