When a target depends on the same generated source file in both PY2 and PY3 modes, it's arbitrary which one wins in the runfiles. Here foobar depends on source file a.py and generated source file b.py through both PY2 and PY3 binary targets. In the runfiles, a.py symlinks to the source file, which is the same in both modes, but b.py symlinks to the file generated in the PY2 output root (the one without "-py3" in the path), silently ignoring the PY3 one.

genrule(
    name = "b",
    outs = [":b.py"],
    cmd = "touch $(location :b.py)",
)

py_binary(
    name = "foo",
    srcs = ["a.py", ":b"],
    main = "a.py",
    default_python_version = "PY3",
)

py_binary(
    name = "bar",
    srcs = ["a.py", ":b"],
    main = "a.py",
    default_python_version = "PY2",
)

sh_binary(
    name = "foobar",
    srcs = [":script.sh"],
    data = [":foo", ":bar"],
)