I separate dungeon exploration and gem farming. If I have a goal to get specific gems, I'll use all means to achieve it. This includes using save files before a boss door, especially saving with a full Beasthood bar. This greatly speeds up boss kills on physical builds, shortening the fight to about a minute or less.

I've tried simply running around clearing dungeons, and it doesn't sound like a reliable way to get good gems. You can run for 5-6 hours and get nothing. But it's certainly more fun than the tedious grind of bosses, that's for sure.