It's hard, not much unused space our runners. I'm sure you know little has changed in the 5th Gens, interior is the least changed thing from 10-21 models. One is the center console ( under the front cup holder) pops out pretty easy, nice little void there for incidentals, but I wouldn't want to do it on a daily basis, risk breaking a clip. The other is the rear wheel well " trays" can be popped out, you have to break the screw to do it though. Once open there's a good bit of room in the passenger side, the drivers side has your inverter in it and it takes up space. Both will clip back in pretty secure even with the broken screw. Lastly is the drivers side jack storage cubby has plenty of void, enough for lots of careful packing.
I have a locking drawer system in mine, sacrifice some storage in the cargo area though because of it. It's big enough for several long guns if I ever felt the need. No way a German Shepherd could fit back there comfortably on top of mine. It's made of metal, obviously not in penetrable but when my hatch is shut the drawer is almost completely accessible. My theory being you will have to draw a lot of attention to yourself having the hatch open and working that drawer with a prybar or something. I've seen some very low profile ones though that may be only raised up 6 inches or so? That would probably allow you some storage and still give plenty of room for the dogs. It would have to be custom built though I've never seen anything like it commercially available. My unit is not even for a 4Runner, it's actually for a jeep Wrangler Unlimited if that gives you an idea of the size of it