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You can edit config files. I'm not sure why it matters, though. It's configured this way so that you don't get different types of dust and ingots (which don't stack with each other and add hassle to processing and storage systems).
For the most part, when playing with GT, you will get the GT version of the dusts from the pulveriser and other thermal expansion machines. With the mod versions that are in ultimate, GT, TE and railcraft dust/pulverised are all interchangeable with each other. It kinda freaked me out when I started ultimate, but I've gotten used to it by now.