Rebate for sliding doors - help!

We requested rebated sliding doors so we had level access in/out of our lounge room to the deck. Our floor tiling started on Saturday and we noticed the track protrudes maybe 2-3cm above the tile so it isn’t level. Can this be rectified now or is it too late??? Has anyone else had this issue??

We asked for this too (I can't remember exactly what the builder said as it was more the 2yrs ago now) but I think it was something to do with drainage/ water not coming in from the outside e.g. when you hose etc. We hardly notice it now and still have the most beautiful outdoor indoor feel. We used the same colour tiles inside and outside. The outside ones are outdoor rated and a little bit grippy/ for non slip. We have a massive 9m wide bifold opening onto our alfresco.