Two (or more!) separate airlines flying on the same route is the very definition of competition!

I expect that the issue you are referring to is that, if there is a great degree of overlap of destinations served by OA and A3, and there are no other airlines serving many of those routes, that the proposed merged airline would end up with a lot of destinations served only by that single new airline - meaning that they would have a monopoly on many of their routes.

I am sure that the EU and any competition body would have no reason to stop Aegean from flying to AMS (if they wished to fly that route, which is another question entirely)