The difference between embedded and pointed store is in technical implementation only, from the shoppers point of view - the shopping experience is 99% identical.
The advantage of embedded store is that you can have your store up and running on a third party website / webpage in a matter of seconds. You can remove your store from the webpage it is embedded on, in a matter of seconds too.
Domain or sub-domain pointing gives your store a designated url on your own domain and is the recommended method to integrate your store with your own website.
We recommend utilizing embed method on websites / webpages where you can not utilize domain pointing for technical reasons, or if you want to display your store during a certain time period only. For example if you are doing a crafts show and you want to display your store on your profile page of the crafts festival website.
Steve - eez.io support