There's a decent amount of threads here from people with a windowed side panel who have found their graphics temps to be a problem. The issue is that it replaces all of the graphics venting with a window panel and reduces the space between the card and the side of the case (window panel is thicker). A reference cooler, like the one you have picked out, should help this problem but I'd still generally stick with the vented side panel where possible.
As well as the performance advantage, you do have to question the practical need for a windowed side panel. A lot of cases have these to "show off" your components and whether or not you think that is cool or stupid is totally subjective. What isn't subjective is that a Prodigy needs access on the opposite side to the window for the front panel I/O. I've owned two(ish) Prodigys for around two years and I've always had to orient them in such a way that a window panel would be generally unseen as you ideally want to "point" the power button/USB towards wherever you sit.
For the front panel I think you are a bit more flexible, assuming you are mounting the radiator in the top section of the case. The big front fan should in theory encounter greater resistance as it's pulling air from the vented edges rather than straight through so it's likely that you'd have to run it at higher RPM to generate identical results. I have the 200mm Spectre Pro fan myself (the size difference to 230mm is negligible but the 230 is thicker for a greater angle of attack) and you probably wouldn't want to run a fan that big at 100% speed as it's likely to be by far the nosiest component. Having said that, the H100i (especially with stock fans) can be very noisy so it might not be that big a deal.
As some general feedback, if you haven't bought these components you might want a rethink as I believe you can do better for the money. A 750W PSU for example, is a bit of a waste.