I tested with trunk. The above errors are still there, but I also got a
scarier one when requiring esxml-query, reproduced below. To clarify,
this is after running emacs --batch -f batch-native-compile individually
on every file in site-lisp, because that's what my package manager does.

Debugger entered--Lisp error: (error "binding stack not balanced (serious byte compiler ...")
  byte-code("\306\30\307\31\310\32\311\312\10\"\33\311\313\13\"\34\311\314\n\f#\35\311\315\n\f#\36 \316\36!\311\317\11\n\f$\36\"\311\320\11\n\f$\36#\311\321..." [h nl nonascii unicode escape nmstart "[0-9a-f]" "\n\\|\n\n\\|\n\\|\f" "[\200-􏿿]" format "\\\\%s\\{1,6\\}[ \11\n\n\f]?" "\\(?:%s\\)\\|\\\\[ -~\200-􏿿]" "[a-z_]\\|%s\\|\\(?:%s\\)" "[a-z0-9_-]\\|%s\\|\\(?:%s\\)" "[0-9]+\\|[0-9]*\\.[0-9]+" "\"\\(?:[\11 !#$%%&(-~]\\|\\\\\\(?:%s\\)\\|'\\|%s\\|\\(?:%s\\)\\)*..." "'\\(?:[\11 !#$%%&(-~]\\|\\\\\\(?:%s\\)\\|\"\\|%s\\|\\(?:%s\\)\\)*..." "[-]?\\(?:%s\\)\\(?:%s\\)*" "[-]?\\(?:%s\\)\\(?:%s\\)+" "\\(?:%s\\)+" (whitespace . "[ \11\n\n\f]+") string "\\(?:%s\\|%s\\)" ident hash "#%s" function "%s(" number dimension "\\(?:%s\\)%s" ((prefix-match . "\\^=") (suffix-match . "\\$=") (substring-match . "\\*=") (include-match . "~=") (dash-match . "|=") (comma . ",") (gt . ">") (plus . "\\+") (minus . "-") (tilde . "~") (asterisk . "\\*") (period . "\\.") (equals . "=") (colon . ":") (lbracket . "\\[") (rbracket . "\\]") (rparen . ")")) nmchar num string1 string2 unit name] 11)
  (defvar esxml--css-selector-token-matchers (byte-code "\306\30\307\31\310\32\311\312\10\"\33\311\313\13\"\34\311\314\n\f#\35\311\315\n\f#\36 \316\36!\311\317\11\n\f$\36\"\311\320\11\n\f$\36#\311\321..." [h nl nonascii unicode escape nmstart "[0-9a-f]" "\n\\|\n\n\\|\n\\|\f" "[\200-􏿿]" format "\\\\%s\\{1,6\\}[ \11\n\n\f]?" "\\(?:%s\\)\\|\\\\[ -~\200-􏿿]" "[a-z_]\\|%s\\|\\(?:%s\\)" "[a-z0-9_-]\\|%s\\|\\(?:%s\\)" "[0-9]+\\|[0-9]*\\.[0-9]+" "\"\\(?:[\11 !#$%%&(-~]\\|\\\\\\(?:%s\\)\\|'\\|%s\\|\\(?:%s\\)\\)*..." "'\\(?:[\11 !#$%%&(-~]\\|\\\\\\(?:%s\\)\\|\"\\|%s\\|\\(?:%s\\)\\)*..." "[-]?\\(?:%s\\)\\(?:%s\\)*" "[-]?\\(?:%s\\)\\(?:%s\\)+" "\\(?:%s\\)+" (whitespace . "[ \11\n\n\f]+") string "\\(?:%s\\|%s\\)" ident hash "#%s" function "%s(" number dimension "\\(?:%s\\)%s" ((prefix-match . "\\^=") (suffix-match . "\\$=") (substring-match . "\\*=") (include-match . "~=") (dash-match . "|=") (comma . ",") (gt . ">") (plus . "\\+") (minus . "-") (tilde . "~") (asterisk . "\\*") (period . "\\.") (equals . "=") (colon . ":") (lbracket . "\\[") (rbracket . "\\]") (rparen . ")")) nmchar num string1 string2 unit name] 11))
  require(esxml-query)