I'm not 100% sure but I believe group policies are applied as close as possible to the client. So if you have AP's the AP's enforce the policy which means firewall, content filter, traffic shaping and vlan. And if it's a wired client or you just don't have AP's the MX enforces it.
If you apply a group policy to a client then it only affects that client. If you specify a VLAN then that clients traffic will be bridged to that VLAN. Any traffic from that client will be limited, no matter what its destination.
If you are bridging all your users to a VLAN then you could apply a group policy to the VLAN interface on the MX instead, and have it apply a per-user limit for all users going through it to the Internet.
Then WiFi access to the VLAN that the user is bridged to wont be affected - it will only be affected when it goes through the MX to the Internet.