You are actually correct that top up fees (whether over or by stealth) have been banned since somewhere around the early 2000s. Top ups in this context meaning additional cash or other inescapable anciliary fees (such as lunches, consumables, other hours bundled in)
And at the time when that was brought in, a lot of nurseries went bust or were taken over by larger chains.
Because there never was a time when any government provided an hourly rate that met cost of delivery.
Before the scheme expanded (lowered age of eligibility, expanded number of hours, inclusion of other types of provider) then it just about clung on.
But now, with the latest changes, the creakiness has become just too much, and yes top ups are back but usually in the "disguised" form so that everyone can politely ignore that they're back.
People go along with it, because they fear widespread closures (or withdrawal from the scheme) if anyone reported their setting and they were directed to stop the practice. But that could happen.
The banning of top-ups was not a good policy, and should have been changed by the following administration. It's predecessor (c.1998 when top ups were allowed) or its original form (c.1996 voucher scheme) were better, as parents were glad of the discount, and the scheme was simpler for everyone, and costs were more transparent.