i removed my third row too but kept the scuff plate and the side cover.. it looks raised to me but i think i like it raised. everything i put in there is contained. nothing is going to fall out when i open the back. just like in a minivan. see the video i created here. towards the end of the video, you'll see how it looks. i just installed back my cover.
2020 4Runner 3rd Row Seat Removal - step by step - YouTube