That's interesting to hear, I guess Pinafore just doesn't have any automated detection of Fediverse links. Sorry to hear about this, I know a lot of people use it!
Pinafore is no longer maintained, but hopefully Enafore could integrate something in the future?
For what it's worth, a lot of apps now do detect Fedi links and automatically do all the copy-pasting behind the scenes, but it doesn't always work so the manual option still has to be there as a fallback.