so, the "existing trunk vent holes" aren't sufficiently critter proof?
and are these vent holes, actually pressure relief structures for when you close the trunk, or the doors, so there's no compression and subsequent difficulty in getting the door to latch?
I'm afraid if you do build your baffles to isolate the existing trunk vent holes, you're removing the pressure relief portion of them, or their main purpose.
Also, if this is to be done because you want to keep the middle of the trunk large enough to fit suitcases and what not, the issue of even being able to sufficiently seal the baffles, and the reality that the trunk itself is going to act like a big compartment muting the output into the cabin, and the fact that IB subs are not going to move air in a pliable container, like a band pass enclosure will, and you're setting yourself up for a less capable system by design.
It's possible that your implementation of this design will surpass my expectations but we're already talking about making bass in the trunk of a Lexus, which is acoustically isolated already and would require significant modification to get the bass to enter the cabin efficiently, and compounding it with a secondary compartment using infinite baffle loading schemes, that further reduces the output available in the cabin from parasitic losses by the trunk lid's flexure and the acoustic filtering of the Lexus standard, sound control.
I'd look into a piping scheme, where I glassed in the enclosures to either side, and used a duct to port into the cabin where there is room. You'd have to accept the compromises of a fourth-order band pass config, though.
then if that's not working, possibly doing a raised deck with shallow mount subs, to get the speakers into the cabin.
If you must have the IB response, you can do the raised deck with aperiodic venting to the trunk, and get your transient perfect detail that way without needing anything drastic in the trunk.
There are shallow mount subs out that require very little depth, and having them in the cabin directly coupled to the air, may give you what you need for far less work overall.
and who's going to care if your deck is 2.5 inches higher than before?