Is your 700 an ADL or BDL/SPS?
When I couldn't get my blind mag seated correctly, the outcome was pretty similiar to what I am envisioning your problem is. I couldn't close the bolt because it would get caught on the blind mag and the barrel sat high.
Pictures would be helpful.
Have you tried installing the action without any of the magazine stuff in it? If it sits better, that could indicate the magazine is what's keeping it from sitting correctly.
If I remember correctly, they are inletted for 1.25" barrels, so smaller barrels will have some space, but it should still look like the barrel is "in" the trough, not on top if it.. at least that's my experience.