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I have this file. My goal is to scale the object completely flat, which I've done within Softimage, the problem I want to scale the object completely flat but distribute the polygon clusters evenly so the topology is a nice flat polygon, but the topology must not change.

I hope once you load it in Softimage and do a simple scale, you'll see what I mean when I said, distribute the polygon cluster areas evenly.

if you post screenshots you could gain more attention because, I'm at least myself not so curious about your problem...

Agree.

I don't understand what the title means, and I can vaguely understand your question.
I see a link for a quite big obj file, and obj doesn't support more than 1 cluster. So I think that what you call clusters, aren't clusters.

My best guest is that you want to flatten your obj and adjust those polygons that are getting overlapped or having very little area. If I'm correct, I think your best option would be Relax.