Yes, by default all Shopify apps are embedded until you disable the settings. But you can change the setting as per your requirement if you want to make your app embedded on your Shopify you can do that by following the steps given below:
Step 1: Go to your Shopify partner panel, Click Here
Step 2: Then click on the Apps section.
Step 3: Select the app which you want to make embedded.
Step 4: Further, click on of selected app.
Step 5: Click on Manage embedded app under the "Embedded app" and then hit on the "Enable" button.
Kindly let me know if it will not work.
Nick here from Shopify.
Just a couple of questions to help understand what you're looking for better. Can I ask what tech stack you're are using to build the app, and where specifically you would like the app to be embedded in your store?
There are a few different guides Shopify has which might be of value to you in the meantime and perhaps even answer your question:
Hopefully, these guides can help and look forward to hearing from you.
All the best, Nick