I found all the gems without painting them (and I'm almost 50 and wear trifocals and am legally blind without my glasses). If you want to take a chance on crashing the game and having to start over, more power to you. But it IS possible to find them all without painting them. I DID use the gem utility, just to find out what I was missing and where (and because when you're looking for a missing green gem it pays to look in grass and trees rather than on the beach or in the water).
Plus painting the gems won't get you the ones on offshore hidden islands or in chests you can't reach until you can use fire or swim or in chests that only appear if you solve certain puzzles or hidden in areas that you need to use clairvoyance magic or the sphere of clarity to see. And I believe those are probably the gems that give people the most trouble when they're using the gem utility and still can't find all the gems.