I'd get both just to avoid any regret. But I guess it all comes down to your preference...striker fired vs. DA/SA. I like them both. I have two FNX-45s and picked up a Gen 4 Glock 21 a couple months ago. And I'll say that Glock 41 sure is appealing.
Basically, I'm no help. Good luck on your decision.
I have a fnx45t but if I get another gun itl be another hk45. My fnx is great for the taticool factor and looks but my hks are just solid and I don't have any issues with my mags not dropping freely unlike my fnx. But jmo. I'd still get a fnx over a glock though.
There you have it. Go get yourself a FNX45T, A Glock 41, an HK45T and a Scar 17. Might as well through a Scar 16 in there too. :-D
Really though you ought to be thinking about what you're going to be doing with this pistol. If you are going to suppress it and put a Mrds on it than the fnx makes sense. If you're a glock guy and don't plan on mounting an Mrds or suppressor than go with your gut. You can always have the slide milled and get a threaded barrel for the 41 if that's what floats your wagon. In the end its a personal choice and as my good friend always says "you just walked into a crack house and asked if you should buy more crack". Cheers and good luck.
IMO the pistol category only requires 2 weapons. 1 for business (carry) and 1 for pleasure (target/comp.) Even better: one that fills both roles. So don't buy either. Put that money into training and ammo. Or Mexican food and hookers. That's what I'd buy if I had $700 to burn.