Empty margins or shrunken content on printouts usually happen when your actual page setup in GoodNotes is different from the output paper size. Please make sure the size of the GoodNotes pages matches that of the printing paper. For example, if you're printing A4-sized pages, make sure the printing paper is of size A4. Conversely, if you only ever use A4 printing paper, make sure the GoodNotes pages you're printing are all A4-sized. To change the template size for the current GoodNotes page, tap the More (...) icon in the top-right corner > Change Template, choose the intended size from the first dropdown list, then tap a paper template. (It won't work if you simply choose the paper size; you'll need to tap a paper template.)
Otherwise, you'll see shrunk or truncated content on printouts and this is expected behavior.
But why don't I get exactly what's shown in the Print Preview section?
AirPrint on iOS/iPadOS is limited in terms of paper size options and support for any additional printing preferences largely depends on the printer.
If you haven't selected a printer, the Print Preview section shown in the Printer Options popover in GoodNotes assumes that every page of the GoodNotes document will be printed on physical sheets having the corresponding same size. For example, if the document has only three pages of sizes A3, A4, and A5, respectively, then you'll get what's shown in Print Preview if you're going to print page 1 on A3-sized printing paper, page 2 on A4-sized printing paper, and page 3 on A5-sized printing paper.
If you have selected a printer, the default paper size will be Letter (unless your printer supports changing this). What this means is, to get exactly what's shown in Print Preview, the GoodNotes pages to be printed need to be Letter-sized.
For more information, see Set Paper Size With AirPrint on an iOS Device from Canon.