It is a mistake to compare the Factoring Fee and an Annual Percentage Rate (APR). Matching the two is not a complete analysis of the credit transaction. Therefore multiplying a 30 day invoice discount fee by twelve does not reflect a reasonable figure.
When a factoring company advances on a 30 day invoice, they expect to be repaid somewhere well within a 90 day time frame, usually between 27 and 45 days. This means the risk involved is over a short period of time, which allows the finance company to make quick adjustments accordingly. The short leash is reflective of the risk the borrower brings into the equation. A bank on the other hand will make a loan that they expect will be paid over a year or more. They are making a calculation that your business will be the same or better over that period of time. If there is a risk that you might not be able to pay back the loan, no loan.
With factoring invoices, the decision to advance funds is primarily based on the creditworthiness of the debtor. It is your customer who will repay (pay off) the advance (see this). So if you try and compare an annualized rate with a short term rate, you must at the same time compare a company that can qualify for a long term loan and one that cannot. Those two companies are not the same, neither is the cost of funds.