Making Safari’s View Controller always go back in history when swiping back
Whether performing a horizontal left to right edge swipe would navigate to the previous webpage in the in-app browser's navigation history or the previous view controller in the app is something which could be customized by the developer of the app.

So it's likely that you will find one or the other mode implemented among different apps. There's no set standard. Although it's possible for the app developer to provide an in-app setting to switch between the two.

You are right that this has the potential of muscle memory failing on the user by increasing the likelihood of performing the unintended gesture in an app.

Turns out, the way Reeder app is implemented, performing an edge swipe always navigates back to the previous view controller (i.e. out of the browser). As per the current implementation, the behaviour isn't configurable. If you wish to navigate back in browsing history, be careful with the gesture.

You may try contacting the developer and share your feedback regarding the same.