This patch below is what I did, *just* to get comp not to complain about the "missing" .emacs.el.

Then something should be done to make it to compile .emacs, and I'm not sure where or how.

I can't shake the feeling that I'm thrashing around and someone who knows the code could do it faster and cleaner.

diff --git i/src/comp.c w/src/comp.c
index b6072a866e..a8e67bbeb2 100644
--- i/src/comp.c
+++ w/src/comp.c
@@ -4473,7 +4473,10 @@ DEFUN ("comp-el-to-eln-rel-filename", Fcomp_el_to_eln_rel_filename,
   Lisp_Object separator = build_string ("-");
   Lisp_Object path_hash = comp_hash_string (filename);
-  filename = concat2 (Ffile_name_nondirectory (Fsubstring (filename, Qnil,
-   make_fixnum (-3))),
-      separator);
+  if (suffix_p (filename, ".emacs"))
+    filename = concat2 (Ffile_name_nondirectory (filename), separator);
+  else
+    filename = concat2 (Ffile_name_nondirectory (Fsubstring (filename, Qnil,
+     make_fixnum (-3))),
+ separator);
   Lisp_Object hash = concat3 (path_hash, separator, content_hash);
   return concat3 (filename, hash, build_string (NATIVE_ELISP_SUFFIX));
diff --git i/src/lread.c w/src/lread.c
index 0a6e4201e4..b0b08ba872 100644
--- i/src/lread.c
+++ w/src/lread.c
@@ -1716,7 +1716,10 @@ maybe_swap_for_eln (bool no_native, Lisp_Object *filename, int *fd,
     Fremhash (*filename, V_comp_no_native_file_h);
 
-  if (no_native
-      || load_no_native
-      || !suffix_p (*filename, ".elc"))
+  if (no_native || load_no_native)
+    return;
+
+  bool _emacs = suffix_p (*filename, ".emacs.elc");
+
+  if (!_emacs && !suffix_p (*filename, ".elc"))
     return;
 
@@ -1724,5 +1727,5 @@ maybe_swap_for_eln (bool no_native, Lisp_Object *filename, int *fd,
   Lisp_Object eln_path_tail = Vnative_comp_eln_load_path;
   Lisp_Object src_name =
-    Fsubstring (*filename, Qnil, make_fixnum (-1));
+    Fsubstring (*filename, Qnil, make_fixnum (_emacs ? -4 : -1));
   if (NILP (Ffile_exists_p (src_name)))
     {