

You’re talking about a great number of organisations, with different decision makers. It takes time and political will to coordinate and execute this kind of big switch. This needs to happen to become independant from foreign monopolies, but I’m not surprised it hasn’t already happened.
The EU commission decides for some EU institutions. Member countries decide for their own institutions and military. Each country and military has its own labyrinth of bureaucracy with lengthy decision making, and large+complex IT infrastructures. All of this has inertia. And switching cost money, even if it’s possible to save on license cost on the long run.
That’s right, the commission probably isn’t involved on those cases. I interpreted “The EU” literally by including its various components, ie the EU commission, the member states governments, companies and individuals in those countries.
There’s no central “EU government” that decides everything. The EU is not a centralized country, not even a federation. Members states takes many decisions on their own, and often need to approve EU comission proposals.