Assuming you are using CUPS print server, you can do something about it.
Cups allows you to set up multiple virtual printers, even though there is only one physical printer available. You set up the printer definition for the print task, such as landscape, photo, draft greyscale, normal color, etc.
So, go into Cups setup and define a new printer, perhaps Kate-print would be a good name. Set the margins as you need them for Kate and test the setup. In the future, when you need to print using Kate, just select your Kate-print as the printer to use.