The absence of speed and power movements in training is probably limiting the amount of weight you use on the bar. No, you won't gain muscle doing high volume box jumps, but you will potentiate the nervous system to fire at a more efficient, faster rate. By improving nervous system efficiency, you'll improve strength, which increases work capacity at sub-maximal weights to build muscle.
Just Don't Box Jump For Conditioning!
Every exercise requires a risk-reward analysis and box jumps fail miserably when used for conditioning.
Jumping for high reps and pushing the tempo minimizes full hip-extension. Full hip-extension is the primary driver of a solid vertical jump and transfers to activities like sprinting, the lockout of a deadlift, or the end of your squat.
How you practice is how you play. If you use faulty mechanics in training, it's going to show up when it matters most. Keep box jumps where they belong, early in your workout as a power exercise.
Want to do metcon? Use low-impact jumping like skipping rope, not box jumps.