Looking at your screenshot it looks like you have Ubuntu's overlay scrollbars. It's very possible they overflow a few pixels on the editing are hiding the bottom of the line.
I indeed cannot reproduce this on my system, where when I manage to put the bottom line the closest to the bottom of the editing area, I get this:  As you can see, the squiggle underline doesn't oveflow the line boundaries, so is completely visible here. I wonder: does it overflow on your system, or is about 1 px of the whole line missing?
Also, one reason I find the red squiggle hard to see on your capture isn't that one pixel of it is missing but that it has a color too similar to what I believe is the bottom scrollbar. It's kind of unfortunate to have such non-background colors around an area containing unknown content. Sure, Scintilla could have a padding, but that would waste screen estate for nothing. A workaround could be changing the color of that underline (not currently configurable unfortunately) or of that scrollbar.
However, we could indeed set [the Y caret policy](http://www.scintilla.org/ScintillaDoc.html#SCI_SETYCARETPOLICY) with an offset so the last line is never on the bottom, something like `SCI_SETYCARETPOLICY(CARET_SLOP | CARET_STRICT | CARET_EVEN, 1)`. I guess that'd be reasonable, but may require a setting. Also, note that if scrolling past the last line is disabled, this won't help with the very last line, as there are none to display below it.
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