This is a tough one!! I have a pair of the old model Asics Hyper Xcs flats. The material is mesh with polyester lining inside of them, so not a breathable as a mesh only shoe. The size 12s fit me perfectly. The Pirannah's in a size 12 are looser... almost too loose. I had to snug up the laces on the Priannahs, which was uncomfortable on my heels after 10 miles. The discomfort was from pressure, not because my heel was rubbing. I think this is because the mesh gives more than the other shoe's construction. If I were to purchase another pair of Pirannah's I would go to a 11.5 size. Also, if your feet are pretty tough, you can just wear sock liners alone.
If you can return the shoes, you might want to purchase two pairs and return the ones that are not right.
Edit: Matt forgot to really answer your question on trainers versus flats. I would go down 1/2 size, because most people wear a thicker sock with trainers. Best bet is to try them on. Check and see if there is a specailized running store near year. I find it much easier to find running stores, than hiking gear stores. Plus the running stores usually have some pretty knowledgable people working there, because they are runners.