A more than 10% shareholder cannot use the Per Diem method under an Accountable Plan for lodging, meals or incidentals. Automobile would be handled as Mileage. I don't understand "tools/equip?" because the corporate would not pay someone for their personal tools except under a Rent/Lease agreement, in which case your shareholder gets a 1099-Misc reporting this as income. And to meet the rule for Home Office means there is no corporate office and there are other qualifications that preclude some of what you listed. Yes, the rules are due to change again in 2026. But not all the way back to pre-TCJA.
The reimbursements are business expense, the same as if the business bought them directly, when paying under an accountable plan. If anything, the anticipation of these types of expenses are already part of operating budget expense, or would decrease net income for the K-1 (if not considered before running the scenarios). The S Corp "owner" isn't writing these off. The S Corp is incurring them. Accountable Plan simply means indirectly. That's part of why this was a confusing comment.
"reduce the net income on the K-1 by the amount of the reimbursements?"
