It's only relevant if there's a loss.  You CAN create or increase a loss with deductions that would "otherwise be allowed" (i.e. on Schedule A for your personal residence).  So entering things in the "top" section allow you to create a loss with those deductions.  If you're taking the standard deduction (or perhaps state taxes are limited to the $10K) then the expenses that would not "otherwise be deductible" go in the bottom.  Still deductible as a home office expense if there's a profit but NOT allowed to create or increase a loss.

Rick