In the versions prior to v3.8.0fx8 an appearance of superscript text impacted the line height (and a gap between lines). Now the problem is solved, but you faced with a drawback of the solution.

It can be worked around either by explicit setting of line height to a greater value (overriding the default line-height: 1.2) or by a decreasing of the superscript font size:

pd4ml-footnote { font-size: 80% }

You may add the style to the document itself or with pd4ml.addStyle() API call.