rust etc on flanges won't matter much and just sand/grind most that off of it... Twisting is the main problem and can/will likely break when mounted. If not now then metal stress from twisting will cause it to break, often soon.
GM for V6 used welded tube manifold about same as Header but not like Headers on many other engines that often have enough tubing between weld joints to take odd loads for heat cycling etc. V6 exhaust manifolds break very easy to start. If flanges are > 1 to maybe 2
mm out of flat plane then forcing flanges to the head will likely stress the part causing fail.
Manifold "Gaskets" won't "eat" much space to make up the difference for un-flat surfaces. Many can barely seal a flat surface on exhaust parts.
Example: 87+ L4 exhaust gasket is a very simple stamped metal piece.
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Dr. Ian Malcolm: Yeah, but your scientists were so preoccupied with whether or not they could, they didn't stop to think if they should.
(Jurassic Park)
The Ogre's Fiero Cave