I've been commuting around 60 miles a week for 8 years now and my experience is soreness comes and goes though there's really two issues: pain and soreness.

Pain or muscle stiffness: is directly related to flexibility and bike fit. There's periods of time where something will hurt or be sore. The single best thing for that has been yoga and/or taking breaks from riding.

Soreness: is from muscles being tired. There's periods where I can ride 7 days a week and never really be sore and times where I really need to avoid riding on the weekends to give the muscles time to rest. I doubt this ever fully goes away. I suspect that if I was very conscious of taking it easy all week I could make sure it didn't happen, but sometimes you just need to go fast.

Take care,

Rob