It will still fit. Installed mine last month and the little tray still fits on top just fine - just like it did before. This safe is fantastic - have both versions installed now.
Oh, and no swear words with either installation. I'm not the best at installing stuff like this, but all went...
I was missing mine, too. Dealer didn't attach it before delivering my truck. None of the Rangers on the lot had one (to avoid theft, I suppose), so I didn't notice at first. That and the 47 lbs of air in the tires didn't make for a very good delivery experience at my dealer...