The fuse_ctrl_filter.sv file includes this at the top:
// Include the generated access control table.
`include "caliptra_ss_includes.svh"
That svh file lives in src/integration/rtl (and is part of caliptra_ss_top_defines). I think the problem is just that the fuse_ctrl item in src/fuse_ctrl/config/compile.yml needs to depend on caliptra_ss_top_defines?