That depends on your code.
You can write one single code featuring the required compile directives to match all or you break up your code in dedicated modules which can be included according to PLATFORM_ID.
PLATFORM_ID is available at compile time, but project.properties is agnostic to that since it’s not used at compile time but before to that to distinguish what to tell the build environment to do.
You can add the dependencies for both platforms, but only include the required ones in your code.
BTW, can you elaborate what kind of differences in dependencies you expect to need?