This is one of the key features of Maven: that it produces a uniform product from uniform parts. If your 2 different copies of that particular dependency are not identical, then you've lost that guarantee of a uniform product.
I have one project that references something like 5 different repositories. There's a lot of overlap, since several of them allow dual use as your one-and-only repo as well as adding their particular product goodness. If it was a scramble between all these repositories for copies of dependencies, it would be a nightmare of the worst kind. As it is, I don't have to worry about which repo a given dependency gets pulled from.
An IDE is no substitute for an Intelligent Developer.