Thread necro here, but I'm running into the same thing...
going to place an order from Tischer soon, and because I have OCD I was going to order the "missing" tools even though I probably am not "supposed" to have them. If nothing else if the open end wrench is anything like the ones in my old E28's tool kit, it's Heyco brand which are really nice wrenches (I had a set at work the last time I actually got paid to work with my hands, years and years ago, and learned to respect them even though they feel flimsy.) Above and beyond that the 10/13 is a very useful size -and it's less than $5, surprisingly. That is part no 71111182747 according to both realoem.com and Jason from Tischer.
However, I just had to do some sleuthing about the sunroof crank/allen wrench. It wasn't listed in the "car tool" section of the catalog, but it WAS listed in the sunroof section. That part number is 54107199321, which is a whopping two bucks. So you can fix two of those unsightly missing recesses in the tray for under $10 plus shipping.
Edit: gotta change my profile, yes I bought the car
What I'd like to know is what the last recess was intended for, the little icon molded in there is completely inscrutable. To me it looks like a SD flash memory card. Fuse puller maybe? My owner's manual does not list contents, and the picture just shows the tow eye, screwdriver, and wrench - doesn't look like it even shows the crank/allen wrench although it is mentioned in the sunroof section.
Edit2: Picked my order up from Tischer on Sat. and the part numbers for wrench and sunroof tool above fit perfectly in my tray so you can use those to order. I have no idea what the last recess is for however. Also picked up the spare wheel/tire/jack kit and some rubber floor mats at the same time. Hopefully I'm almost done spending money!