Same deal when Chrome opens mailto links in gmail.com in the browser instead of my default mail client. Stuff like this made my switch to Firefox even more of a no-brainer.
I am totally pro-Firefox, but your case is not about Chrome being a bad actor. For websites to be registered as link handlers, the user gets asked and has to accept (like camera access)[1]. There is no difference between Chrome and Firefox in this case.
[1] https://blog.hubspot.com/marketing/set-gmail-as-browser-defa...