This may help. https://graphicdesign.stackexchange.com/questions/199/point-vs-pixel-what-is-the-difference, so yes, a point is always 1/72nd of an inch in applications regardless of what resolution (dpi) your printer prints at.
As you mentioned, “…the long edge of a 8.5"x11” piece of paper will only support 792 pixels." This should hold true across applications. If you measure in pixels, inches, centimeters or postscript points, the numbers change in the measurement increments used in the inspectors and the ruler, but what fits on the printed page hasn’t changed. It is the same size, no matter which increments you chop it into. If you print 14pt Helvetica from TextEdit, Pages, and OmniGraffle, you should have the same text at the same size from all of them. That is because there are 72 points in each inch no matter where you are printing from or what increment you set the ruler to. Part of the reason this is so confusing is many written resources use dpi and ppi interchangeably, although they aren’t the same.
Printers have points (can be imagined as dots of ink) and never pixels. That means pixels have to be converted into points when you print. That conversion isn’t changed with screen resolution or by what resolution your printer can output. When talking about printer dpi (dots per inch) we are talking about how many dots fit inside one inch, which is more like density than size. It is still one inch total, no matter how many dots go inside of that inch.
Surely there must be a way to make this better!
Canvas Scale in OmniGraffle Pro
In OmniGraffle Pro, you have the option to change the Units including the scale. This means you can try setting the Scale in the Canvas Inspector to 1pt = 10px or whatever ratio you want. 1pt = 2.43px is about as close as you can get for the example above. There’s more information in the OmniGraffle Help if you search for “Changing Ruler Units to Suit Your Design Needs” and “Canvas Scale”.
Page numbers that use the page number variable are based on how many pages will print. The printer you target in Page Setup defines how much content can fit on a page based on the page size set, as well as the margin required at each edge that the printer needs to grip the paper internally (to move it through the printing process).
When you set your scale to Pixels, the default Scale is 1pt =1px which means there are 72 points per inch, therefore where you have 72 pixels you get 1 inch of content on the defined page. When you set your scale to Inches-Fractional, you still have 72 points per inch. In OmniGraffle Pro you can change from that default to define a scale either exactly or as a ratio.
Page Setup Scale Percentage in OmniGraffle Standard
If using a different scale in Units doesn’t suit your needs, or if you are using OmniGraffle Standard, try using the scale percentage (Under the File Menu, choose Page Setup) at lower than 100% temporarily, only while you are printing. That way you can set it to 100% for pixel usage, and scale it down so more contents will fit on the page when printing. For your example, try somewhere between 40%-45%. Give that a try, and see if it gives you a bit more control than the Print canvas on one page checkbox. If you want to define your pages based on the content, try making a layer for each “Page” and use the <%layer%> variable. That way your numbering is controlled by the layer name and not by the printed page definition.
These are some techniques that could work, but I know there are many UX designers who measure in pixels & also need to print. Hopefully some other OmniGraffle users will share what works for them in case I missed a useful tip.