NPOs do not need to use MACRS. Most that I have seen use straight-line. But if MACRS is used, make sure the category selection is correct (the $100k renovation is probably not 15-year property). I don't think the NPO can use Sec 179 or bonus depreciation, unless the property is part of UBTI.
Of course, the $100k goes on their books - how would you have complete books without it?
Some NPOs may be required to show depreciation as part of their program costs to certain agencies or donors, for example, or if they have audited financial statements.