I have seen them mounted in the trunk before. Someone made a wooden panel that bolted in place of the cloth that covers over the window to the soft top storage, and then bolted the amp to that. I've also custom wood trunk floors that have had amps mounted to them.
I made a panel that blocked off my back seat and carpeted it as I have a bubbletop, and built a small sub box into it. I mounted the amp to the soft top. However I ran into issues where the amp would overheat and hit its built in thermal cutoff, there's very little airflow there as it turns out. Something to keep in mind if you're going to mount under the seats