This bug may be specific to the "noinclude" code path

Indeed it is

The specific cause of this issue seems to arise from twinkleprotect.js#L1487 (and the code for other content models just above), in which the version with a <noinclude> tag doesn't have a \n automatically put at the end of its tag text.

I would say to just add a newline to keep the same behaviour with or without the noinclude text, but I'm not sure if that could screw up tagging on template pages, where bringing in a sudden newline at the top of the page could potentially break output (I don't personally use twinkle so I'm not sure how realistic of a scenario this is, or if the newline could even be problematic in most scenarios), so I won't be submitting a PR to add it myself for now

Reported again at https://en.wikipedia.org/wiki/Wikipedia_talk:Twinkle#Missing_line_break_when_protecting_AFD_page

I was able to reproduce on an AFD page

A good algorithm for the fix might be to just look for == at the top of the wikicode. If this is found, add a line break when doing the prepend.