The most common reason for large gaps at the end of a page is due to the macros being unable to BALANCE the columns. Usually stretching the length of a paragraph on that page (or to a paragraph that should be on that page) by just one line solves the problem. Sometimes, depending on the text within a paragraph, you can REDUCE the length by one line makes it fit.
Either of these can be achieved by using an Adjust List - accessible on the View+Edit tab/page. Use the Generate… button to create a list of paragraphs, and then change the +0 to a +1 to grow or or -1 to shrink a paragraph. It isn’t always possible for a paragraph to grow or shrink, so this takes some time and effort.
If balanced columns are not important at all, and you just want the text to use all the available space on the page, then you could add these two lines to your ptxprint-premods.tex file (accessible from the Advanced tab) and it will ignore column balancing.
And you could always examine the “unbalanced” output afterwards and then stretch or shrink columns to manually balance the pages.