I am getting the exact same error and using the same setup for my application that you mentioned you are using for yours.
We were getting this error first:
Unable to get the private bytes memory limit for the W3WP process
But then we ran both of the following:
metaacl.vbs IIS://Localhost/W3SVC/AppPools IIS_WPG U
and this
aspnet_regiis -ga <WindowsUserAccount>
We then noticed that the user account to connect to the network share where the application source files are located was not under the IIS_WPG group so we added it and now we see the warning you mentioned.
Did you get or find anything on how to solve this?