diff -up src/sage_setup/command/sage_build_cython.py.orig src/sage_setup/command/sage_build_cython.py
--- src/sage_setup/command/sage_build_cython.py.orig	2020-10-30 16:04:33.325411659 -0600
+++ src/sage_setup/command/sage_build_cython.py	2020-10-30 16:09:19.770071485 -0600
@@ -262,6 +262,9 @@ class sage_build_cython(Command):
         with open(self._version_file, 'w') as f:
             f.write(self._version_stamp)
 
+        # Remove buildroot paths from the generated files
+        subprocess.run(["find", "build/cythonized/sage", "-type", "f", "-exec", "sed", "-i", "s|@@BUILDROOT@@||g", "{}", "+"], check=True)
+
         # Finally, copy relevant cythonized files from build/cythonized
         # tree into the build-lib tree
         for (dst_dir, src_files) in self.get_cythonized_package_files():