Yes, the $50 penalty for failing to file Form 8606 is technically triggered when the deadline passes without the form being submitted. This means the fine applies in both of your scenarios.
The law allows the IRS to waive the fine if you can demonstrate reasonable cause for the delay. You can attach a brief letter explaining that the omission was an honest oversight and that you are correcting it to ensure their cost basis is accurate. If you take this approach, the IRS may process the form without the bill. There isn't a guarantee they will do so, but often they'll accept the letter.