Do an owner's deferrals have to be considered when calculating the 5330 penalty for untimely deposit of employee deferrals?

Why would the "timely deposit" requirement by applied any differently for owners?

In fact, in a preverted sense, a participant could almost make a case that this was discrimination in terms of benefits rights and features in a downward market (i.e. the employees contributions are being invested immediately as the market drops, the owners contributions are being held as cash equivalents and are not dropping in value. Therefore, the non owners are losing money while the owners are not. The owners will invest later when the market bottoms out).

I know that this is not the specific issue that you are addressing - but I don't recall that the timeely deposit requirement makes any distinction between owners, HCE's, Trustees, NHCE's, KEYs, non-Keys, etc. or whatever.

All deposits must be made timely - period............

I agree with actuarysmith.

The owner could be "trapping" the contributions in the plan sponsor to keep the interest income.

Also, I'm sure that the IRS would impose the prohibited transction tax, even if it only involved the owner.