Placeholders Should Not Pop to the Front
On a slide master or layout, place a logo or other static content over top of a placeholder. Now make a slide from it and fill the placeholder. The placeholder is now on top of the logo. That's wrong. This is a long-standing design flaw that needs to be fixed.
This suggestion is not the same as the idea of adding layers to the slides, please do not amalgamate this with that idea.
Prakash F commented
Yes, Let the user decides how he wants to order his objects irrespective to master or normal views.
In other words, when you add content to a previously empty placeholder, it should retain its original z-order position.