I'm not sure I quite understand the issue here but my comment is to open seams and stitch in the ditch. If you are sewing in an open seam, surely the needle is bound to hit those threads. Hence, the chance of breaking the thread in the seam. If I chose to press open, I would not do stitch in the ditch quilting for that reason. Don't be afraid to press seams open--remember when we were doing garment construction and we pressed the crotch seam open. Those didn't seem to break but then we weren't sewing over that seam either! Only with time and stress did those seams pop open.
I have to comment about cotton vs polyester fabrics. Some quilters are so particular about all cotton fabrics, being "pure", but then machine stitch the finished product. I do like the sheen and the durability of cotton/poly blends and they tend to not fade like 100% cotton. Like you have experienced, cotton wears.
As with all crafting, do what you like. You are really the only one who is enjoying the process.