It shouldn't be possible to run reftests locally if the manifest isn't hooked up to the build system. (The fact that it's possible leads people to forget to hook up their tests.) We should probably fix this by replacing use of "include" in manifests with listing the manifests in moz.build files.
This would be fairly straightforward to handle like the other test harnesses--like you said, remove the master manifest and generate it as part of the build from the set of REFTEST_MANIFESTs from moz.build files. We'd need to write a little code to generate a reftest manifest, adjust the mach command to point to the generated manifest by default, and change test packaging to package the generated manifest.
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