When encrypting the text from the "Clipboard" (oh, what a name! Shouldn't it be
called ANYTHING else to prevent confusing it with the clipboard? Our followers
coming from PGP would be confused, because PGP actually has an option to encrypt
the real system clipboard!) the text is encrypted in such a manner that when
decrypted on other systems (say Windows), the line endings are messed up.

gpg has a "-t" option specifically for text encryption, to deal with this issue.
(At least when encrypted with this option, PGP for Windows does show line
endings correctly.) Since we know that "Clipboard" definitely contains nothing
other than text, it should be safe to use it when encrypting "Clipboard". Or at
least I believe we should be given an option to do so, which I have not seen
(correct me if I was not looking well enough). And I still believe it should be
enabled by default - for "Clipboard" only.