Exccessive contribution must be returned. You cannot pay a penalty and keep the money there. Usually your plan will return your excessive contribution before 4/15, those amount will be included in your gross income, but no penalty if returned by 4/15. I think if the 401K plan returned your exccessive contribution, your company should have gotten the matching back too. So it's as if you didn't overcontribute at all, but a lot more paperwork.
Your problem is that you have two jobs so at the plan at each job the contribution is less than the 20500, but when you received the two W-2s the IRS will know your contribution is over 20500 by adding up W-2. So then you'll get a penalty.
I don't suggest you overcontribute in this situation.