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I am afraid I don't know Pepakura (have heard of it of course). I use Blender because I have known it for years and working with paper-models-add-on for unfolding is so easy now.
I have worked with Sketchup for a while and I believe it's a very good app with a great intuitive approach on designing stuff in 3D. If what you are getting from Pepakura back into Sketchup are the actual parts as objects, I think it should be doable to "bend" them where you want across score lines. But it's a step you have to do manually. The only challenge I see is when you have a build step to illustrate where a section is assembled already, you will probably need to delete the glue tabs there, as they might result in rendering artifacts when being in the same place as the area that is glued to them.
Good luck and I look forward to see your results!
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