Assume the employer makes HSA contributions for those employees who participate in the employer's HDHP.

The penalty, as I see it, for not meeting the HSA comarability rules is an excise tax equal to 35% of the amounts the employer contributes to all HSAs for that calendar year.

If that's correct, why couldn't an employer exclude everyone from the HSA contribution program except the sole HCE? Rather than potentially paying mucho bucks to other employees' HSAs, the employer is simply stuck with a small penalty based on the HSA contributions made for the one HCE?

Is there something I'm missing?

Not at all; this seems doable (.35 x HCE contribution = exceise tax). Presumably, the employer will still get its deduction under IRC 162. It might be more advantageous, in this situation, to just make a personal contribution to an HSA and claim deduction on Form 1040