I ended up enabling the -C option so that it creates a MyApp.ctf file in addition to the MyApp executable instead of embedding the .ctf contents in the executable. On first run, it extracts the files to MyApp_mcr directory. Since I'm building a Docker image, I run extractCTF MyApp.ctf to create the MyApp_mcr directory when building the image. I wish I could then delete the MyApp.ctf, but it errors out if I do.
mcc help -C Do not embed the deployable archive in binaries.