I'm now hitting this too, on nearly all the compiled modules in the stdlib. One example:

building '_codecs_jp' extension
x86_64-my-linux-gcc -m64 -march=core2 -mtune=core2 -msse3 -mfpmath=sse --sysroot=/opt/my-generic/0.0.1-dev/sysroots/core2-64-my-linux -fPIC -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -I../Include/internal -I. -IObjects -IInclude -IPython -I/usr/include/x86_64-linux-gnu -I/usr/local/include -I/usr/include/python3.8 -c cjkcodecs/_codecs_jp.c -o build/temp.linux-x86_64-3.8/cjkcodecs/_codecs_jp.o
x86_64-my-linux-gcc: error: cjkcodecs/_codecs_jp.c: No such file or directory
x86_64-my-linux-gcc: fatal error: no input files
compilation terminated.

I think the working directory is incorrect at some stage - note that the first two -I would make sense from Modules, but the next three do not.