in your linker script (and the resulting binary), addresses are just addresses.
Whether these are meant virtual or physical solely depends on your loader (which might be a tiny bootloader at early system init that doesn't know about virtual addresses or a full blown OS that provides a sophisticated virtual environment).
So it's the program that brings your binary into memory that decides whether addresses are interpreted virtually or physically, not the linker script.
Unless you tell us about your specific environment, we can't tell you more.