The point a user reaches on the page by scrolling is recorded as a Percentage ([total number of visitors]/[maximum depth scrolled to on your page]). This means it's not an exact distance in pixels or otherwise, but an average of depth.
On a shorter page, visitors will hit a higher percentage with less actual scrolling, and potentially a lower average in longer pages. When Hotjar generates the Scroll Heatmap and processes all the maximum depths scrolled, we end up with an average that will be applied to the Heatmap.
The Heatmap should be a good proportional representation, even in pages of varying lengths.