First, to state the obvious, a SEP is a type of IRA that employers contribute to, and plans may allow employee contributions to it. Then,
Because you say this is a self-employed SEP: this would be used for those businesses reporting on Sch C (sole props, disregarded entities) or partnerships on Sch E, and those contributions are considered contributions by the individual and are reported as an above-the-line deduction that comes from line 16 of Schedule 1, and that is why it is being factored in on the Roth limitation worksheet. Does the return have an entry on that line?
It would be different if your client was a W-2 employee of his own company (a C or S corp): employer contributions would not be taken into account for the limitation you asked about, but if client as the employEE contributed to the employer plan, then those would factor in to the Roth limitation.