Whether that has any practical difference given the nature of politicians and politics in general, well, at best your mileage may vary.
If they didn't wanted that, they could have blocked it. However, leaving EU might actually help the government to have a better localised excuse. For example, maybe child abuse is not a big thing in your country but immigration is a hot topic? Then you can have "break the encryption to stop the human smugglers" campaign.
In France, there's an election for each. One for national parliament seats, one for EU parliament seats.
In the last decade, the national elections were usually won by center-left (Macron's party) while the EU ones were won by the far-right (Le Pen even has a seat at the EU parliament AFAIK)
Over in the UK, the EU can't stop the new Kakistocracy from actually doing it. I know where I'd rather live.
And then EC bureaucracy has a lot of weight with appointed commissioners (who frequently know jackshit about assigned fields) acting as PR figures.
That being said, things like this would happen at the national level for sure, the EU has nothing to do with it. It's systemic to "modern democracies ".
In the EU enforcement is mostly decentralised, anyway.