The short answer, explained
Backdating isn't a discretionary penalty HMRC chooses to apply; it's how the registration rules work. Your legal obligation to register arose on a specific date once your turnover crossed the threshold, and HMRC's job is to identify that date accurately.
This means even if you apply months late, or HMRC only spots the issue during a compliance check, your VAT registration is treated as having started from the correct date, not from when the paperwork catches up.
The same principle can work in your favour for voluntary registration, where in some cases you can ask HMRC to backdate to an earlier date than your application, provided you can evidence you were trading and intending to make taxable supplies from then.

