It appears that tilde means something to the asciidoctor tool :) which affects the markup in undesired ways, "opening spans" of unexpected length and potentially not representing the author's intended text (dropping ~ in generated output). One such occurance can be seen in manual/installation.txt:45 (HTML output "simply delete the ..."), haven't systemantically searched for other spots.
This must be something which depends on the asciidoctor(1) version. It was observed with 0.1.4, but does not reproduce with 1.5.4. Closing the report.