It reduces the attack surface (you can't break into the phone by plugging something into it)... which also means that jailbreaking will be a bit more difficult.
It also completely removes them from the debates and regulation of connectors. Lightening? micro usb? usb-c? All of that goes away.
By removing cords and cables it also removes the "my device doesn't work because I was using a flaky 3rd party cable" ongoing support questions.
> The MagSafe Duo Charger conveniently charges your compatible iPhone, Apple Watch, Wireless Charging Case for AirPods, and other Qi-certified devices. Just place your devices on the charger and a steady, efficient charge begins on contact. The charger folds together neatly so you can easily take it with you wherever you go.
They'd need to move the entirety of the wireless power transfer devices and accessories to some other standard.
In the scenario you describe, the EU wants Apple to remove a nonstandard lightning connector and replace it with a standard one for increased interoperability and decreased e-waste.
It looks like what you describe is exactly what happened, which is exactly what the EU wanted.
Why do you think it's a bad thing?
Do you think governments mandating that analog telephones used RJ-11 and twisted pair to be bad?
What about mandates on electrical receptical standards?