Happens all the time. The SEP rules are in 408 and right on the 5305-SEP form itself, but they are either not read or ignored. IRA custodians such as fund companies, brokerage firms, etc. don't "administer" SEPs, they simply hold the IRA accounts, it is up to the employer to administer the plan, and they are frequently administered just as this owner suggests.
I know IRS knows about it, I've told them myself. but these things fly beneath their radar. They'd rather beat up an employer who forgot to sign a minor interim amendment to a 401(k) that had no impact on plan coverage or contributions, rather than track down the rampant abuse in the SEP world that results in a federal tax expenditure for the owner's contribution and no retirement benefits at all to other employees.
<rant/off>