To prevent employee to access ALL SHOP , you need to do some custom work in the file to disable the ALL SHOP for employee role.
Inside admin-dev/themes/new-theme/template/components/layout/shop_list.tpl , you need to add a condition at line no 39
{if !isset($current_shop_name) || $current_shop_name == ''}
{if $employee->id_profile==1}
{l s='All stores' d='Admin.Global'}
{/if}
{else}
Not tested but this is something you need to play with to hide the ALL SHOP for a particular profile in Prestashop.