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You are correct that a more permanent mount would be better. I kind of liked the idea of being able to remove it with no trace left but a couple of buttons would be minimal. I am sure there would be more than a couple of BN1/2 folks who'd love a drawing of your compartments. At least in my case you wouldn't see the pile of spare bits I carry.Hi Roscoe--
I like what you have done thus far and wonder why you don't make your LR semi-permanant with bolts going up through the boot lid into threaded inserts, etc? As shown on the red and white car it's a nice look and is certainly safer than straps and cups, etc. Four small chrome buttons to fill the holes when the rack is off is not a bad look.
All that said. I can fit a lot of soft luggage in the boot of my car, with tools, spares, fluids and odds and ends stowed in their own compartments beneath the flaps as pictured. As I recall I used 1/2 sheet of 3/4" MDO and one 8' length of HD continuous hinge. I'd be happy to send you a full-size pattern of the floor and flaps when my car comes back in a couple of months.
See: https://www.britishcarforum.com/community/attachments/bn1boot-jpg.58307/
With regard to boots, I wonder if anyone has bothered to address the fact that unless you are using the bias ply tires that are like original, most radial tires don't want to fit very easily in the space alloted for the spare due to the vertical dimension of the space being too small for modern tire sizes. I used to have to shove the inflated tire in with a big foot ( what better to use in the " boot") and pulling it out was most unpleasant so now I just insert it partially until it is firmly wedged and leave it at that. I could leave it partially inflated but that kind of defeats a quick wheel and tire change by the road side. One of those small 12V compressors might be the fix for doing it that way but with my luck I'd have a flat battery along with a flat tire. Fix-a-flat anyone?