Well, flipping the motherboard would force you to think out a new I/O location and expansion slots as well. I had a look at your Acrylic case and to me it looks like a fulltower or something in between?
I'm all about bottom mounted PSU's since they don't get in the way of hot air rising inside the case. Yes it can be a difficult reach for your cables but open the right holes and there shouldnt be any big problems. If it does, extend.
Since youre building the case from scratch my bet would be to just decide on what location and work my way from there. Your creation looks promising nonetheless.