Yeah, Security Keys definitely illustrate that "more convenient" isn't "less secure". Signing in with a Security Key is so painless, it's just a shame I can't do it in more places.
Use the clipboard as interprocess communications for secrets does seem dangerous. The 'pass' password manager I use has an option to do that if you want that, but I've rarely used it. However it may be less dangerous than you realise - by default pass will destroy clipboard items it added after 45 seconds. This is easy on X and, as far as I know, any modern graphical desktop, because the "clipboard" isn't (usually) really a static buffer, it's a live negotiated relationship between desktop clients, so "pasting" is an operation in which the copying software is itself actively involved, so if it were to crash, the content is gone, not left on the clipboard.
Use the clipboard as interprocess communications for secrets does seem dangerous. The 'pass' password manager I use has an option to do that if you want that, but I've rarely used it. However it may be less dangerous than you realise - by default pass will destroy clipboard items it added after 45 seconds. This is easy on X and, as far as I know, any modern graphical desktop, because the "clipboard" isn't (usually) really a static buffer, it's a live negotiated relationship between desktop clients, so "pasting" is an operation in which the copying software is itself actively involved, so if it were to crash, the content is gone, not left on the clipboard.