I can't see why a custom resolution would harm the graphics card. If there was any harm I would expect it to be with the monitor. The main negative is the custom resolution isn't natural to the display resolution so won't look as clear. How important clarity is will depend what you're working on with Adobe.
Personally I have a 1680 x 1050 monitor running a custom resolution of 1920 x 1200 on a GTX 750 ti. Nothing bad has happened to monitor or graphics card after several months.