Back to the original topic, I may keep my eyes out for creative solutions (I like the idea of padding and some type of carpet as mentioned above) but I'm not worried too much about covering up the holes. It wouldn't look even close to OEM anyway, so I just figure might as well not bother. If someone were handy enough and wanted to put in the effort into creating a custom-molded plastic piece that mounts to the OEM trim with clips or something that seems semi-OEM, I'd be in for that at any reasonable cost in a heartbeat. Not holding my breath, though...
And to veer back off topic, I don't think my interior rattle has anything to do with the third row seat removal. It's a very minor hard plastic rattle-vibration type noise that can only be noticed at low speeds (before road noise covers it up) and I'm pretty sure that it's coming from the interior of the tailgate. It sounds like that hard plastic piece that bridges the tailgate and cargo area floor just resonates a bit. Has anyone else noticed this? I can't imagine that if you drive at low speed (under 15 mph) with radio off, everyone's cargo area is totally silent. The pieces back there just seem like they would all make a little noise. I've tried a bunch of other things in the cargo area just trying to narrow down the source and it hasn't done a thing. I took the tool kit out today just as an experiment and that made no difference. Ugh.