CTRL Shortcuts Don't Work with Mac

I'm using a Microsoft keyboard on a Mac, and I'm having trouble changing shortcuts using ⌘ to CTRL in Illustrator.

Because my keyboard settings are ⌥=Windows Key and ⌘=Alt to more closely match my PC at home, pressing shortcuts like ⇧+Alt+V for Paste in Place can be difficult. 

When I attempt switching Alt with CTRL, I get "The key pressed cannot be used as a shortcut" message.

If this is because Mac keyboards use the ⌘ key like the CTRL button on PC, I'm confused about why Mac keyboards still have a Control button separate from ⌘, except for very limited and specific functions. 

Maybe these functions are what's keeping Illustrator from assigning shortcuts to CTRL, but I don't know what they are.

Normally I would attribute this CTRL issue to Apple wanting a different experience than PCs. But interestingly, once I deactivated the "CTRL+ →" shortcut under Mission Control, I was able to use it as a custom shortcut in After Effects. Is there something about Illustrator in particular that doesn't like CTRL? 

I realize this is more of a question about the Illustrator user experience than a bug or problem, but any insight is greatly appreciated!