So my question is this writing of waypoints an EASA requirement and what EASA rule is this based on
No. If it is a requirement, then by the operating manual of your company. That again has to be approved by your national authority which itself operates according to EASA rules. If your company can come up with an alernative procedure, your authority might approve it.
But I really don't understand your problem. If you get a direct-to-waypoint clearance, you read the ETO of that waypoint from your FMS and enter it in your flightlog. When passing the waypoint (ten minutes, twenty minutes or an hour later...), you check the estimate against the actual time over. Two seconds of your time consumed that would have otherwise been spent dozing. On a one hour flight, that leaves you with about three time checks to do. Back in the old days (not so long ago!) without those direct-to legs we had to do it 35 times per hour!