The point a user reaches, by scrolling on a page, is recorded as a Percentage using this formula:
[total number of users]/[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, users will hit a higher percentage with less actual scrolling, and potentially a lower average in longer pages. If a user clicks a link that takes them to a lower point on the page, they are still included in the scroll data because this will be based on the furthest point reached by the user.
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.