Your accountant did their job. You wrote off what you were entitled to write off, your taxable income came down, and that is the entire point of hiring a good accountant. Then a W-2 underwriter opened the same return and read it as "does not earn enough." Both of those things are true at once, and only one of them is a problem.
It qualifies you on money that landed in your account instead of on the income line of a tax return. Typically 12 or 24 months of personal or business bank statements. The lender totals the deposits, applies an expense factor to account for the cost of running the business, and uses the result as your income. No tax returns on most programs. No W-2. It is not a loophole, it is a documented, fully underwritten loan that simply measures income a different way.
These programs price higher than agency. That is the deal. What you are buying is qualification you would not otherwise have, or a purchase price that actually reflects your business. Whether that trade is worth it is a math question, not a sales question, and it is one we run before you apply. If agency wins for you, agency wins, and I will say so.
On most bank statement and 1099 programs, no. That is the whole point of them.
12 or 24, depending on the program and how the file looks. 24 months usually prices better.
The percentage a lender assumes it costs to run your business, deducted from your deposits before they call the rest income. It varies by industry and by lender, and it can often be lowered with a CPA letter. Getting this right is most of the work.
No. A decline is one lender's answer under one set of guidelines, it is not a permanent record. Most of the self-employed files I close were declined somewhere else first.
Whether a bank statement program beats agency for you is a math question, not a sales question. We run it first. If agency wins, agency wins, and I will say so.