What you are doing here is actually stereo with bundle adjusted images, and not bundle adjustment with mapprojected images, as I see it.
The tool fails because of the following. Bundle adjustment decides the name of the output .adjust file based on the camera file. In your case you have no camera file, so it uses the image file, which is image1.tif. But later, when you do stereo with mapprojected images, like:
stereo image1_mapped.tif image2_mapped.tif run/run --bundle-adjust-prefix run_ba/run
you are offering the tool neither cameras, nor original images, so it gets confused.
I am not sure it will work, but you can make a copy of your .adjust files in run_ba to look like this:
run_ba/run-image1_mapped.adjust
and hope that it will pick them.
Also, a bug was fixed recently where imag1_mapped.tif did not remember the RPC model from image1.tif. If you have a build without this fix, when you do stereo with mapprojected images but no bundle adjustment, so like this:
stereo image1_mapped.tif image2_mapped.tif run/run
it will still fail, and in that case you'd need to get the daily build from GitHub (in the release area).