there is currently no way of having the project's settings in the IDE be applied to the project when running with loop_*. However, there are ways around it. Usingh the Bela_userSettings function one can set default settings for a project. These would get overridden by command line options, but when running with loop_*, no command-line options are passed. If the program is a C++ project, you can add a function in your .cpp file as such:
void Bela_userSettings(BelaInitSettings *settings)
{
settings->periodSize = 512;
}
if it's a Pd project, you should copy the core/default_libpd_render.cpp to your project (where you already have the _main.pd file and add settings->periodSize = 512; to the function void Bela_userSettings(BelaInitSettings *settings) which is already there.