L of the W, I'm with Montegue here. But first off I have found that most tool trays have been damaged after being installed the wrong way around and this puts the jack directly over the diff and it doesn't need much suspension travel to make contact and cause damage ie. the famouse hole it creates in the deepest part of the jack aperture.
There is plenty of space in the rear, by and under the spare wheel to store the jack with a little ingenuity and there is a tool box available in metal that fixes to the rear lip of the spare wheel carrier frame where it attaches to the chassis cross member. By the addition of a clever securing pin I have seen the jack secured inside the frame holding the spare wheel screw clamp. It stayed in place by opening the jack to fix it tight in place!
Depending on your model the under bonnet area of the drivers footwell is often free of any thing mounted by MMC and you can easily fit a tool box of your choice to this area using RIV nuts to secure it through the bottom of the tool box which is isolated from the body by rubber washers, 3/4" tap washers are good here. You can lock it and pad your tools to stop rattles.
Now to the real problem, the tool tray itself! MMC must have got Cadbury's to manufacture it on their milk tray box line as to be honest its next to useless. and if fitted with tools as supplied let alone anything extra you may wish to carry has the integrity of a Tesco carrier bag! It bounces up and down creating one hell of a din and when the suspension is asked to do any work crashes anything in it making the Mog sound.... well, like a bag of spanners!
A good way to sort things here if you wish to delete it, is to replace it with 3mm clear macrolon sheeting (shatter proof). Screw it down using the original fixing holes in the frame and it produces a water resistant finish. Return the ply floor piece as per normal and access is as simple as before and the quickly removable ply panel allows a visual inspection of the rear axle/battery area if needed without needing to remove tools then tray! Oh! and no more crashing noises, You will be mightily impressed just how much quieter the car is!