Another problem I have is that there is a metal panel under the boot parcel shelf). But there are some holes (for the standard-speakers) in it. I'll first try it that way

What kind of box dor you have the sub in? if it was something like a band pass box the options are better. Maybe you could get a suitable box (crutchfield?) and take a flexible pipe from the open port to neatly into the rear shelf holes. It could be installed well and unobtrusively.
This would possibly affect the tuning of the box but give you a great increase in sound.

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Murray