is it less secure to have the key store outside of the C:\Users\$username$ folder?
No, it isn't less secure. However If you are keeping your key store on your machine once compromised any location on that machine is no more or less secure. It may be slightly more secure depending on the nature of the attack vector. Though this would only be security through obscurity as you are essentially hiding your key store. Though this is presuming the attacker is using a script that can only search for the key store in predefined locations.
However if you are creating duplicates of your key in multiple locations on your machine then you are essentially making it easier for an attacker to find your key store.
I am aware that to compromise a wallet, both the key store file and the associated password would be required.
Yes this is true, but it is far far easier to brute force attack a password than try to brute force your private key. And if the attacker is using a key logger then then you may expose your password to them without the need for brute force.
I'd recommend that you use a hardware wallet if you are trying to get maximum security.