Yes, this should work alongside the Discourse Subscriptions plugin without any issues.
The embedding relies on configuring specific parameters to control what topics are displayed, such as category, tags, or per-page, through the d-topics-list tag in your website’s HTML. If your embedding ended up framing your whole forum, you might want to make sure that the Discourse URL and any parameters in the <d-topics-list> tag are properly set to reflect the topics you intend to display.