To get rid of the dialog, just tick the checkbox:
"Do not show this message."
and then 'No' and you will not be bothered again.
This is a user-settings, so each new user gets the dialog at least once.
This setting is stored in a binary file:
%APPDATA%\Microsoft\WebManagement\7.0.0.0\InetMgr.preferences
so it can not be easily set by your server-setup script, which is unfortunate.
Also you can not remove the link to the "Web Platform Installer" in the actions pane. If you decide to download on the server you have to click through tons of IE popups telling you that is not a good idea to download anything on a server.
If you don't want 'junk' on your server, why did you install IIS Manager in the first place. It is not really needed on a server. But that really depends on your whole setup.
Without IIS manager there is also no WPI popup.
Having said all that, if you are using many of the components that WPI allows you to download and install, it can make your life much easier.
I sometimes use WPI on a workstation but never on a server where everything is scripted.
In the end it takes two clicks to get rid of it on every server, but I would rather not have it popping up. The link is enough.