This does sound like a bit of a tough one. It seems like you are working through your options well, flat housings for the smaller items would likely be the best scenario. The softer more pliable nature of the acrylic paint presents some pros and cons in this situation. On hand it will be flexible which could be an advantage for rolled storage; however, it is malleable, i.e. deformable, which could be a significant problem. I’m hopeful that we’ll be able to get some folks with expertise in the realm of modern paints and/or painted textiles to weigh in on this issue.
It sounds like you’re on the right track of thinking with regard to rolling face out to place less strain on the painted surface and using an interleaving to protect the soft paint film from abrasion of the backer. Additional questions that come to mind for me would be what is the potential of changing the surface texture or sheen by having it in direct contact with the Mylar under the pressure of the weight of the rug? Also, would there be a concern for migrating plasticizers to be affected by the contact with the Mylar resulting in a different appearance than the segments in flat storage?
Thanks for such a great questions and a complex issue, I think it could spark some useful discussion here on the list.