I'm currently working on an application that will interact with Shopify merchant stores. For those wanting to connect their store against our application, they would need to use their user account from our application server. This functionality is a bit similar like connecting your store against Facebook or Instagram.
I'm aware that there is a standardized flow when installing plugins. However, I would like the user to log into our application after installing the plugin but before getting the access token. That way, we can just store the token immediately and get data on an on-going basis.
This isn't a question on whether this is possible to implement, but whether this is appropriate to implement. Especially if the plug-in is only dependent on our application.