I can also reproduce this without the additional configure flags:

[cpython]$ git clean -fdx
[cpython]$ mkdir -p build/debug
[cpython]$ cd build/debug
[debug]$ ../../configure --with-pydebug
[debug]$ make
[debug]$ cd ../..
[cpython]$ build/debug/python -m test -v test_tools
...
SystemExit: ERROR: missing _freeze_module

As well as from the build dir:

[cpython]$ cd build/debug
[debug]$ ./python -m test -v test_tools
...
SystemExit: ERROR: missing _freeze_module

But when I build from the source directory directly:

[cpython]$ git clean -fdx
[cpython]$ ./configure --with-pydebug
[cpython]$ make
[cpython]$ ./python -m test -v test_tools
...
Tests result: SUCCESS

Hence, I assume the culprit is in building from a subdirectory.