My advice is to try to fix it if it bugs you but that it doesn't detract from the feeling you are going for. It looks great! Keep it up!

Are those windows (and the "red section") physically a different layer that sits on the larger prop?
I've seen flickering like that when you have two overlapping  (or superimposed) planes, and the graphics card has a hard time knowing which one should be visible.

If they flickering parts are simply part of the same larger diffuse texture map, then I don't have any good ideas.

I sure hope you get this figured out.  I love that opening sequence.  It's really awesome!

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iClone 7... Character Creator... Substance Designer/Painter... Blender... Audacity...
Desktop (homebuilt) - Windows 10, Ryzen 9 3900x CPU, GTX 1080 GPU (8GB), 32GB RAM, Asus X570 Pro motherboard, 2TB SSD, terabytes of disk space, dual  monitors.
Laptop - Windows 10, MSI GS63VR STEALTH-252, 16GB RAM, GTX 1060 (6GB), 256GB SSD and 1TB HDD

You can see the flickering at 13, 17 and 50 seconds.WOuld a better card help? I'm using an Nvidia GeForce GT 610

I thought about going Indigo, but it's just too much! 200 frames was 60+ gigs and just exporting it took all night. If I'm going to do this with Iclone, it will have to be through a card for now.

https://drive.google.com/file/d/0B2DqqAmBEs_GRkhSZm1aMXU5YVk/view?usp=sharing