Am I allowed to deduct those expenses?
No, not as a deductible rental expense.
If so, can I deduct those expenses as part of the Safe Harbor?
No, because there's no doubt those improvements are "a permanent and physical part of" the structure. So cost doesn't matter.
Do they go as improvement?
They must be entered as a property improvement in the Assets/Depreciation section. They get classified as Residential Rental Real Estate and depreciated over the next 27.5 years. Depreciation starts on the date the work was completed, as that will be the "in service" date.
