The issue was that we were manually specifying the mount point as FPaths::ProjectContentDir(). This was originally done because we also mount custom-built .pak files that include text files, and this setup worked fine — until we disabled the Share Material Shader Code option, which caused the internal structure of the .pak files to change.
It turns out that if we set the mount point to null for .pak files generated by UE, everything works correctly.
Thank you — your explanation pointed us in the right direction and helped us resolve the issue.