How to map a terminal command to a function key

The easiest way might be to disable the Fn key. Since you say that using Fn+F10 works, you could go into System Preferences > Keyboard > Keyboard, and enable Use all F1, F2, etc. keys as standard function keys. This way you no longer need to press Fn to send F10.

The second solution is on the PC side. You could install a utility such as AutoHotkey on your PC and remap the keys there. That way the keybindings will only work on the PC. Lifehacker has nice looking tutorial about this. In AutoHotkey, you can decide which applications the shortcut applies to, but in your case it seems like a global hotkey would work since it is running on the PC side.

Another solution might be to try one of the ways to create keyboard shortcuts menitoned in this Lifehacker article. This article's goal is to help you do similar things that AutoHotkey let's you do on the Mac.

Remapping a Windows keyboard so that the key positions match a standard Mac keyboard is pretty easy.

Just open Keyboard Preferences, and click the Modifier Keys… button in the Keyboard tab.

This lets you change the behaviour of the keys on each attached keyboard (make sure you select your external one from the top drop-down menu).

To turn the Windows standard Ctrl⊞WinAlt configuration to the Mac standard controloptioncommand ⌘, just change the Option and Command drop downs so they have the opposite entries (i.e. Option performs Command and Command performs Option).

If you want to change the physical keys, most of the premium mechanical keyboards use Cherry switches that have interchangeable key caps. You can get Mac specific modifier key sets from places like DAS Keyboard and WASD Keyboards. If you want to go nuts, you can even get a fully customized key cap set in a style similar to Apple's keyboards, as this guy did (looks pretty nice IMO, but I'm sure it's costly).