1: policy-ID check in the VPN is different than "unset ike policy-checking" . Please check https://kb.juniper.net/InfoCenter/index?page=content&id=KB16008&actp=search
http://kb.juniper.net/InfoCenter/index?page=content&id=KB9518&actp=search
2: policy-ID check in the VPN comes in to thepicture when tuneel is established however "unset ike policy-checking" helps to bring the tunnel up. Check KB https://kb.juniper.net/InfoCenter/index?page=content&id=KB6744&actp=search
3: unset ike policy-checking is global command and indeed affect the all the VPNs.
Thanks,
Vikas