Fear not, there are THREE custom made trunk "separator" or organizer options made for the lower trunk, as well as numerous trays made for the upper shelf, such as the one you link in your original post.
Among the 14 Vics I've owned, I've used or bought just about all of them. First I'll start with the lower trunk organizers.The Ford Kelvar Police Trunk organizer:
They are the most common you'll find, but still they are hard to lay your hands on because they are bulky to ship. So when you find on Ebay, they'll almost always say "Pick-up only". I once wanted one so bad I contacted a seller in North Carolina who had three, I asked him to nest them together, shrink wrap them and not box them and just take 'em to Fedex for bulk shipping. He did, shipping was less than he expected for even one, I got them fast, kept one, sold the other two to guys in the local club for a small profit. If you can find one locally, they cost about $150. Plexiglass covers are hard to get in good condition. They're not that smooth in the rear trunk, the edges stick up at award angles. Supposedly they offer a bit of rear end crash protection.ProGard partitioned organizer:
These are really good, with a large single hinged lid and many movable internal dividers. They sit flush in the bottom of the trunk and can be covered with matching carpet to make a semi concealed lower trunk. Again, they are hard to find, hard to ship. Expect to pay about $150. Marauder Town Car organizer:
These are the best, they sit flush and have clever accordion hinged lids that open in multiple ways, plus internal dividers. They were standard on the Marauder and some Town Cars, optional on the Sport and other Marquis. New, they were only $100 from Ford, but you'll pay over $200 today if the seller knows what he's got. Shipping is likewise a nightmare.
Side Storage/Forensic Boxes:
They come in two sizes, larger and smaller, for right and left sides, respectively. These can frequently be had on ebay for $40-50 apiece. I like them as they make for useful places to store first aid kits, fire extinguishers, etc. Shelf trays:
These come in A LOT of different sizes and from different manufacturers. From full width sliding shelves that will hold the tire, to half shelves that go on the left side of the tire. The half shelves were designed to mount extra electronic equipment and slide out, they are more useful than the full trays, in my opinion, because with the tire on the full tray, it becomes so heavy that it's hard to unlock or disengage to slide it out and I haven't found it to be too convenient. The half trays are about all you need, just keep the spare where it is at.
Hope this helps.