It has always been this way .
VSE installs the agent in "Updater" mode, so it can update and run scheduled tasks.
Managed environments now wanting to manage those systems simply push the agent install to it, and the Agent will 'do the right things' to then talk to your ePO server. But if you have difficulty with this task you'll want to chat with the McAfee Agent folks (use ePO forum).
Thanks for the quick reply! I figured it would be something like that. We usually install the McAfee Agent first then install VSE 8.8 afterward. So in that scenario where the agent is already present would the VSE installer install the version that it was bundled with or just leave it alone because the agent is already there? Also if I were to Deploy the Agent from ePO to a machine that has had the VSE 8.8 P2 full installer ran on it manually and now has Agent 126.96.36.1992 would the version of Agent I select via the Deploy Agent command overwrite the Agent that was installed via VSE 8.8 P2 installer?