Hi,
It is yes. When you select a menu item in that setting, the checkout will automatically add the parameter &Itemid=XXX to the URL of the checkout where XXX is the id of the menu item you selected.
Then, the SEF system of Joomla uses that Itemid parameter to automatically replaced component/hikashop by the alias of the menu item.
There is only one condition to that: The menu item needs to be of one of the types of HikaShop.
Otherwise, if Joomla were to replace the component/hikashop part of the URL by the alias of the menu item, the link would actually display what you selected in that menu item. So if it's a listing of Joomla articles, you would see that listing of Joomla articles when going to the checkout.
So just make sure that you select a menu item of HikaShop in that setting and you'll see it will work like you want.