latency_measure: Fix bug where the wrong prj.conf file was used

Fix a bug in the latency_measure sample where, when the board was
specified through the environment, the wrong prj.conf file was
selected.

This change is not a pure refactoring, as it is believed that there
have been some copy-paste mistakes where prj_small_freq_divider.conf
and prj.conf have become out-of-sync over time. These assumed mistakes
are not carried over in the new organization.

Signed-off-by: Sebastian Bøe <sebastian.boe@nordicsemi.no>