On my '96 W140 Coupe, the large opening came from the factory containing a plastic package containing 5 lug bolts that match the front alloy wheels...
The front and rear wheels on my Coupe have different offsets... and the front and rear lug bolts are different lengths.
The spare tire/wheel is an alloy that matches the "front" with 51mm offset. According to the owner's manual, if you have to replace a flat front tire, just use the original bolts.
If you have to change a flat rear tire, you're supposed to use the bolts in the tool kit with the spare... and repair/replace the flat tire as soon as possible.
If you have four identical wheels on the car, and the spare is matching ... my guess is that the space is supposed to be empty.
Not sure what the small hole is, but I agree with Gilly about its intended purpose for the wheel key. That's what I use mine for.
Can post a pix is anyone's interested.
Hope this helps. KenP