It's true that the larger your volume of transactions, the cheaper the per-transaction fees are for direct deposit/debit when you use a 3rd party to originate your transactions. Most financial institutions transmit directly to the Federal Reserve Bank (FRB ) with the few exceptions being very small community banks and some small credit unions, but this requires an up-front investment which would probably be cost-prohibitive for a small business.
For businesses who don't want the up-front costs (and the requirement to use software named "FEDLINE" from the FRB on a totally closed system), there are plenty of companies out there who will originate your transactions for you. They typically charge less than a dollar per transaction, with NO percentage fee based on the dollar amount of the transaction.
I just did a quick search, and Bank of America offers this service, but their website doesn't have pricing. It's probably based on volume and/or business account balances. There's another company (paysimple.com) and they do it for $0.55 per transaction, no matter the dollar amount of the transaction.
At 55 cents per transaction, that means that it would be cheaper to use paysimple.com instead of paypal as long as the payment amount (including reimbursement) is larger than $18.97 (0.55 / 0.029 = 18.97). Therefore, as long as the MSC's
average payment amount is larger than $18.97, they'd save money by using paysimple.com. If the MSC is smart (and if their software is smart), they will combine all of your shops for the month into a single payment to minimize the number of transactions per month. It's hard to imagine that any MSC has an average transaction amount less than $18.97.
There
are some financial institutions which will originate your transactions for FREE, as long as you have a business savings/checking account with them. One of my former employers offered this service, free of charge, to all business account holders. They even supplied the software for free. All you had to do was enter the information into the software and press SEND. You could also import files from many of the most popular accounting softwares (Quickbooks, Peachtree Accounting, Goldleaf, etc) to eliminate manual data entry.
I'd be willing to bet that Bank of America and most of the other large banks probably offer lower prices than paysimple... probably with pricing that depends on the balances in your business accounts at the bank. The large banks have such a huge volume of transactions going to/from the FRB that the per-transaction fees that they pay are so small that it's easy for them to make money while charging very low rates.
As an example of Bank of America's economy-of-scale... an individual with a checking account at BofA can use their checking/savings account at
any other bank or credit union in the USA as a source of funds for paying their bills via the BofA website. They can also transfer money freely between their Bank of America account and their accounts at other financial institutions... all from BofA's website... and all for free. BofA does this by originating debits/credits through the FRB... and they don't charge you a dime for that service... because they pay such a low fee per-transaction that it's worth it for them just to provide this extra service to make their customers happy.