In order to get the ships to render properly, you will need to make a minor change to an in-game file called "HemisphericalLighting.vsh" (don't worry, this is SUPER EASY). You can find the file from desktop mode in the .local file (the folder will only appear if you select the "display hidden files" option in the file manager. Once in .local, open up the steam folder, then steamapps, then find the treasure planet directory and open it. You should find the VertexShaders folder, open that, and then open the "HemisphericalLighting.vsh" with a text editor. If you don't have a text editor by default, there are text editors available to download in the discover store that's built into the steam deck on the bottom left of the screen (the one I used is called Atom). Once you have the file open, erase all the text in the "HemisphericalLighting.vsh" file, then save the file and close (don't delete it!). Open up the game again, and everything should work fine now (ships are now rendering properly!).

For improvements to controls, I've made a new Treasure Planet Battle at Procyon community control scheme for the steam deck that you can use (complete with virtual menus and button layouts). I've also altered the touchpad mouse ping rate, so the cursor will be much easier to use (similar to what you have to do to get the mouse working on PC). I've labeled most of the buttons as well. It's been through a trial run of the first few missions, but feel free to modify the controls as you wish. I haven't seen anybody else make a custom control scheme for this game on the steam deck yet (possibly due to the rendering issue, which can now be fixed!) so it's the only one on the community layouts list at the moment.