tl;dr please set NO_NACL_GOMA=true. Sorry for annoying messages.
The hacks in build_nexe.py GetGomaConfig may do something bad for you. If either of followings are set, build_nexe.py try to use gomacc. Goma is used only when it confirms compiler_proxy available but you may see annoying messages shown by the checks.
1. use_goma is set in GYP_DEFINES environment variable or something equivalent.
2. GOMA_DIR environment variable is set.
3. gomacc can be found in PATH environment variable.
As you can see very beginning of the function, NO_NACL_GOMA=true kills the feature.