Under full documentation, an underwriter starts at the bottom of your return, not the top. Gross receipts are not qualifying income; net profit after expenses is. Vehicle costs, home office, equipment purchases, travel, and owner benefit all reduce that number, and most of them are entirely legitimate.
Some of those deductions are added back — depreciation and certain one-time items are non-cash or non-recurring, and guidelines allow an underwriter to restore them. Many are not. The distinction between what is added back and what is not is where two lenders can look at the same return and arrive at different qualifying income.
Income is also normally averaged, commonly across two years, and a declining trend is treated more conservatively than a rising one. A strong current year does not fully offset a weaker prior year, which is why timing an application around your filing schedule matters more for self-employed borrowers than for salaried ones.
None of this is a reason to change how you file. It is a reason to know which figure a lender will use before you make an offer on a house, so that the qualification conversation happens on your schedule rather than during a contract period.