If you have already installed the profile — no, you can't move modules by modifying make file. Profile's
.make file is used only during installation process.
If you want to replace modules from
sites/all/modules on already installed copy of Drupal, you can just replace files (with
mv or something) and then run
system_rebuild_module_data() function to ask Drupal to update modules destination. With Drush:
drush eval "system_rebuild_module_data();"
For profile installation process — I really don't know why and don't know how to modify
.make file. Maybe you can specify
'contrib_destination' property for every project...