This is "by design" (for better or worse).
The only workaround at this stage is to use JavaScript that can target this particular message. Trying to hide it using CSS is a bad idea as it will apply to all status bar messages which are very important for end users to see.
There's an example script on Sohel's Blog:
<script type="text/javascript">
ExecuteOrDelayUntilScriptLoaded(hideWarning, "sp.js");
function hideWarning() {
var statusbarContainer = document.getElementById('s4-statusbarcontainer');
if (statusbarContainer != null) {
var messageSpan = document.getElementById('status_1_body');
if (messageSpan != null) {
if (messageSpan.innerHTML.indexOf('The current page has been customized from its template.') == -1)
statusbarContainer.style.display = 'inline';
}
}
}
</script>
There's also a post worth reading about this on TechNet forums called How to hide Revert to Template Status on the SPD Customized Pages. Particularly the response from Dalibor MSFT shows options for dealing with this.