cmake: use zephyr_get() and zephyr_file() for APPLICATION_CONFIG_DIR

Fixes: #73065

Update APPLICATION_CONFIG_DIR is Zephyr CMake and sysbuild to follow
the common principle in Zephyr for relative paths.

This means that relative paths are taken from the application source
directory when specified on command line, and require local scoped
defined APPLICATION_CONFIG_DIR to be given as absolute, for example by
using CMAKE_CURRENT_LIST_DIR.

Signed-off-by: Torsten Rasmussen <Torsten.Rasmussen@nordicsemi.no>