My sub installation is built in below the OEM panel rather than a replacement overlay. Much cleaner install, and you can't tell it's modified at all. Course there's not enough air space for a 12" so you would have to stick out to accomodate that. My installtion was all about cargo space, convenience, tight deep bass and stealth. Others will choose differently
I always hated having to take out a sub box everytime I haul something.(been there done that..) Where to put it while your moving things. You aren't always near the garage when you have to use the trunk sometimes your just out, then what..... Besides we don't have garages here in THE city.
In any case, the point of the original question was how to put the sub in and accomodate the 3rd row simultaneously. And to address the original question, there is enough space in the side compartment if you choose the right sub. Some are designed to need less air space and perhaps one designed for a small and ported enclosure could need even less space allowing for a larger driver. I did mine in 98 when I first bought the car so I'm sure there are new ones out now. You should really consider a skilled install technician to help you design and install it properly.
I think I also looked into one that fits where the BOSE sub sits under the drivers seat. You could consider 2 smaller subs under the 2 front seats which being closer to you will sound very loud also.