Yes you are able to setup an SCS server separately. Then at a later time use the SCS Add-on to integrate it into SCCM.
It's absolutely possible to have full AMT functionality without using certificates. You can achieve full AMT functionality with a basic SCS profile. That profile only needs to contain the mandatory system settings. Later, if you want, you can go back and reconfigure your vPro computers with a new SCS profile that includes any of the increased security options.