Programmatically add pane to panel page

Im using panels and panelizer and it's all good! I really love the module.

I actually like it to an extend that I would like to more or less skip the page.tpl layout and just print the content region.
However, I would not like to add breadcrumb, tabs and various other elements to all my panel pages via the UI. Mostly because editors might remove the panes when using panelizer.

Is it possible to programmatically attach a pane to a panels region somehow? I have been looking through the various alter hooks without any luck.