Green flags where waved after the safety car went into the pits meaning 40.13 does not apply as there was no safety car or safety car conditions to inforce the rule.
Excessive and unclear regulation is the problem which restricts racing and results in shitstorms like this. If any national racing club can geta championship through a season without having most of the races end with an unclear/dubious result, then why can't the FIA manage it with F1?
The cars may be faster and more complicated but the same basic rules apply, as for technical regulations, they need to be simplified and loosened too.
That is not true, most series has rule controversy shitstorms. (Mostly resolved in the same way, race control is right even when race control makes a mistake)