Depreciation for office in home is on Line 42 of Form 8829, which then gets entered on Line 30 of Schedule C.

Depreciation for two rooms rented in home might go on Line 13 of a separate Schedule C, if you are reporting this as a business, or on Line 18 of Schedule E, if it is just another rental. 

The amount of depreciation for each 100sf room should be the same, unless one or more rooms were added at a later date.  You might not be able to claim all the 8829 depreciation, if the business shows a loss.  You might not be able to claim the Schedule E loss, if your income is too high.  In both cases the depreciation gets carried over to a year when you might be able to claim it.  

I have no idea why you would say "It's obviously more beneficial to count on Lin 13," so you must be smarter than I am.  It's obvious to me that it's the same amount regardless of where entered.