You could still run into all sorts of issues.
If you have any issues with your e-gate card then you will face problems when you present a passport to the immigration officer that is different to the one that is paired to your e-gate.
Also when checking in for your flight back to Dubai, you would be presenting a passport at checkin which will contain different data to the one that EK hold on file for our staff travel.
My advice is don't give this any thought as you may seriously regret it if things go wrong.