It’s a bit strange that the employer wouldn’t use the maximum exclusion, because if they are willing to pay $5000 toward your loan, but only treat $3000 as tax excluded, they also have to pay a little bit extra in employment taxes.
however, one of the hallmarks of this type of employee benefit plan is that it must treat all employees fairly and equally. Maybe the company has decided that some employee positions are not valuable enough to deserve the full $5000 of tax free assistance, and if they limit the assistance for some, they have to limit the assistance for everybody.
