@Mistuke says:

autoconf 2.70+[1] have several backwards incompatible changes in them. Since msys2 follows Arch Linux's package philosophy it'll always be using bleeding edge. Because your github actions is installing msys2 fresh it'll get latest autoconf which is 2.71.

So it's not really a Windows issue, you can get the same error on Linux with a new enough autoconf. You should be able to fix it by setting AC_CONFIG_AUX_DIR to the directory containing the config.guess and config.sub.

[1] http://git.savannah.gnu.org/gitweb/?p=autoconf.git;a=blob_plain;f=NEWS;hb=97fbc5c184acc6fa591ad094eae86917f03459fa