The feedexplorer module is installed automatically into the admin folder, so you can't remove it from the install / module folder.
What you can do however is set it to a premium module so that the module is not accessible to the portal.
To do this, log in as host, go to admin menu / site settings
advanced settings / host settings
In the premium modules section move the FeedExplorer from the selected modules to premium modules.
You should be able to set this up before DotNetNuke is installed, checkout:
Configuring DotNetNuke before installation
(How to create a portal site template for the wizard)