I don't think bigger biceps can be a bad thing.
The squat example is wrong. Muscles cant lengthen and shorten at the same time. It's about net lengthening, a muscle that is stretched will want to contract, if its not stretched at the end of the eccentric, it won't be a prime mover.
There is an arguement that hamstrings only activate in a deeper squat where there is a net lengthening. In the squat the hamstrings pull the tibia posteriorly to anchor it against the anterior pull of the quads, allowing the hamstrings to continue contracting to extend the hip. I think rippetoe wrote about this.
The difference in the bench example is that the biceps won't be stretched to the same degree as the hamstrings would be in the bottom of a squat and so will have no reason to contract.
Does that make sense?