I'd like all modules in my Agda library to be compiled with the --prop command-line option. Is there some configuration file where I can put default options for my library?
You should be able to use the flags: field in the library's .agda-lib.
The test case for the feature is precisely --prop: https://github.com/agda/agda/blob/ebf922e06c3d1e86ae3cd4cc99cbe9ac8bc5648a/test/Succeed/default-flags/lib.agda-lib
It's all in the manual: https://agda.readthedocs.io/en/v2.6.2/tools/package-system.html#library-files