Minimal example of custom standalone JUCE Projucer project.
Run it in Debug to see some messages printed to the console that let you verify indeed StandaloneFilter.cpp is used, and further customization by returning a different StandaloneFilterWindow implementation is possible by modifying StandaloneFilterApp::createWindow in StandaloneFilter.cpp.
The messages you should see are
Instantiating StandaloneFilterApp via our very own StandaloneFilter.cpp
Instantiating juce::StandaloneFilterWindow via our very own StandaloneFilter.cpp