I have a beautiful mavic module e size 700. When laid flat it isnt completely flat to the surface. it wobbles a bit...oh maybe 3-4mm. There arn't any cracks or creases in the rim itself.

Just wondering if it'll be able to true up. Is there any tolerance for which a rim can be trued back?

Its doable with small bends. To get the wheel true, your spoke tension will be off where the rim is bent, so spokes on one side will have to be really loose while the other side really tight to pull the bend straight. I have ridden a wheel this way for many miles without a problem but it was a front wheel and had 36 spokes. I don't know that I'd feel comfortable doing it with a rear wheel or a low spoke count wheel.

There is no set tolerance. 3-4 mm is a good bit of variation. If you want a somewhat stable wheel the rim needs to be gently bent back to a closer tolerance. Otherwise you will have very uneven spoke tension and may have a slight flat spot where the rim is physically bent. There is no way to tell if you will be able to true it in any case.