Isn't that the same with any collection of libraries? If you don't use a framework and just pick your libraries, you'll still need to ensure that their versions work fine together.

If you pick a bunch of standalone libraries you can be fairly confident they're not going to interfere with each other - which version of your web templating engine you use has nothing to do with which version of your ORM you use, and you can upgrade each independently. When they're both part of a big overarching framework it's more likely that a subtle interaction has slipped in and not been noticed.