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When the terminal text reaches the bottom of the window, it's hard to see underscores and font descenders since they're so close to the window border.

Can I configure a blank line (or 2)?

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You could output the terminal control codes ("ANSI codes:, "xterm control codes") to go one line down (scrolling the terminal up by one line when in the last line) and one line up again.

Should be done when the prompt is shown - or possibly as part of the prompt (try this first).

Regarding terminal codes and how/where to output: here's a more complex question - showing something in the line below:

unix.SE: Display stuff below the prompt at a shell prompt?

XTerm Control Sequences

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There's a 1px border by default around the grid of characters. You can increase this value by placing this in ~/.config/gtk-3.0/gtk.css:

VteTerminal {
    -VteTerminal-inner-border: 1 1 5 1;  /* for vte <= 0.36 */
    padding: 1px 1px 5px 1px;            /* for vte >= 0.38 */

The four numbers are for top, right, bottom, left respectively.

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