What are the implications of deducting mortgage interest for rental property in the Assets/Depreciation section instead of the Expenses section?

I do not know the implications of your question.  However, Turbo Tax specifically requested rental property mortgage interest information in the Rental Property expenses section.  The amount I entered there populated on the 1040 Schedule E under "Expenses, Item 12, Mortgage Interest."  Thus I assume "Expenses" is the correct section to record rental property mortgage interest.