I have a six digit new haven left hand Winchester m70 and I’m thinking about swapping out the two piece bottom metal for a one piece Blackburn unit.

Will the factory magazine box work with the Blackburn unit?

Also, their #3 unit comes in a standard depth and extra deep. What’s the difference?

It should work but you will need to shorten it a bit due to the extra thickness of the newer bottom metal.

I'm not sure about Blackburn, but I have Sunny Hill bottom metal that is narrower at the trigger guard and wider at the magazine than factory, so you would have a gap at the trigger guard.