@Kshitij shukla,
If someone installs an App, that App can download theme.liquid using the Assets endpoint. The App can then edit the file and upload it. You probably saw the result.
It is considered to be very BAD practice to do that. You can screw-up and ruin a store. The merchant cannot easily edit your changes, and everything breaks if they change their theme.
So yes, it is possible to embed your whatever in the theme, but don't do it. I would think Shopify would block your App from the App store if you screwed that up too. Any merchants complain about monkey business and your in trouble.