crazy in fact considering there are meant to be free borders.
Ah, well, actually the EU is more about free and fair trade, ie. shipping goods over borders without hassles of VAT drawback/duty, import/export restrictions and such.
If you want free passage over the borders for your own person, what you should be looking for is the Schengen treaty. Which the UK, sadly, did not sign. So anytime you leave or enter the UK you've got the hassle of going through an immigration process. Which is, I grant you, made easier on the UK side through the GAR form, but still a bit of a hassle. On the Schengen side, you've got to go through one of the designated "customs" (although in this case "immigration" would be more relevant) airports.
Once you're within the EU, and within the set of countries that signed up to the Schengen agreement (and that's indeed a different list), for private flight essentially all borders disappear. With the exception of the fact that you need to file a flight plan for any flight that crosses an international FIR boundary. Big deal.