I don't think you can have your cake and eat it too. If you recognize that a decent sub in the spare tire well is going to rattle the thin cover, then if you want the sub in there, it will require a more sturdy cover, very possibly with a cut out/grill. And a grill in the middle of the cargo floor will definitely collect dirt or debris.

If it were me, I'd have a car audio shop build a custom fiberglass enclosure that replaces the removable panel that covers where the audio equipment is. If you want to use a W7, even the smallest ones are fairly deep and would have to be built out a couple of inches. But a good shop could make it look somewhat 'factory'. Or get a flat style subwoofer...they do exist, and will never match a W7, but will still be a huge upgrade. Just make sure the custom enclosure is easily removable in case you need access behind it.

Another option that I used in a prior car was I got a single W7 in a JL wedge shaped enclosure and just kept in the corner of the trunk. If I needed 100% of the trunk for a trip, I just took it out.

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2014 BMW 328i Xdrive
2011 BMW 335i M-Sport
2008 BMW X5 4.8i Sport
2000 BMW 528i 5sp