Intensity is a measuring tool, not something that goes by feel. That being said, you are right, you can front squat a whole lot less than you can back squat. 100% is still 100%. Say you have a max 300lb front squat and a max 500lb back squat. 90% is going to be just as intense on the front squats as it is on the back squats. You are just using different leverages and mechanical advantages/disadvantages.
Your question is which is more important? The actual weight used regardless of movement used or the intensity to which you train in a given workout? The answer is both. It all depends on what your weaknesses are, how far out from a meet you are, how much volume you are using, and a bout a billion other different factors. Instead of making yourself crazy, just got balls to the walls with whatever you are training for that day and do everything you can to improve your numbers on the lifts you suck at.