With the CDs being mastered prior to MorphOS they will automatically point to the default Amiga Installer, so you probably need to adjust where the installer should look to use the MorphOS installer to install the program. Probably it will be enough to right mouse click over the installer and select the MorphOS installer from the options.

I know I've installed Wipeout 2097 on my system, so it's definitely possible to do so, and I think there's a patch file for MorphOS for the game so don't forget to do that as well. Here's a link to Wipeout 2097 files - MorphOS Storage

Hope this helps.