Sadly this is a VERY badly thought out feature. The order that placeholders are populated when you switch themes can only be accessed in the XML code and even then the logic is quite twisted!
IF you understand how to access and edit the XML for the custom layouts the value you are looking for is idx but don't go there if you don't understand - you must use the values that exist but change the placeholders they relate to. Potential for problems is high!
We have several major clients who are pee'd off with this and have asked us to write code to replace "Apply Theme" which makes sure the content goes where it is intended. Not a solution unless you have a big budget!
Sorry I cannot be more helpful.
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