Adding IKEv2 to the list of tunneling protocols wouldn't have an impact on the other connection profile settings that also reference the default policy you are just allowing another tunneling protocol along with the ones you already have enabled.
Although personally I would create a new group policy for the site to site connections just to keep things more organized but if you want to use the default policy that is ok too.
Troubleshooting a failed ISE Upgrade Readiness Tool Assessment
About the Author
Richard Atkin is an Engineer at a Cisco Partner in the UK, specialising in ISE, WiFi & Prime... I'm also currently learning about APIs, Webhooks, AWS, (etc et...
Security Product and architecture introduction-NGFW portflio(8/6)