First of all, how would you normally type a tilde into a Mac-native application (e.g. TextEdit) using that keyboard? It may require the use of the Option (a.k.a. Alt) key. You can bring up the Keyboard Viewer to help you figure out how to type it. You enable the Keyboard Viewer using the Input Sources tab of the Language & Text pane of System Preferences.
Assuming you can figure out how to type it in a Mac-native app, it should work the same way in CrossOver with one caveat. You need to tell CrossOver whether it should use the Option key to access additional characters from the keyboard or to send the Alt keystroke to the Windows programs it is running. You configure that in CrossOver's preferences. By default, the left Option key sends Alt to Windows programs while the right Option key, if your keyboard has one, accesses additional characters.
You can test that the keyboard layout is working properly in CrossOver by running our built-in version of Notepad. Bring up the Run Command dialog and just type "notepad" as the command, and click Run. Verify that you can type a tilde into that just as you would in TextEdit.
If that doesn't help, many games let you reassign the key used to access the console, via their options. So, you can configure the game to use a key that's more convenient for you to type.
I honestly don't know what effect, if any, that registry key you mention has. I'm not sure if a Windows key remapping program will work, but it seems unlikely to work well.