Exact same boat. I found this behavior to be really user hostile as a default. Recently switched to Orion (browser from Kagi), and they’ve got a much more agree

Exact same boat. I found this behavior to be really user hostile as a default. Recently switched to Orion (browser from Kagi), and they’ve got a much more agreeable flow for this. When a link in Orion takes you into another app, there is a popup available when you return to Orion, allowing you to disable opening in the external app. Additionally, long-pressing always provides an “Open in…” option to purposefully choose the GitHub app.