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The short answer is; it can.
When you get your first individualized education plan from the school, it will have a primary and secondary (if applicable) disability. This should be an indicator of where your child tested in the evaluation stage.
The primary has a couple of functions. It gives every future teacher of your student a heads up about where they are and what they need. It can also be pivotal in placement decisions. For example, kids with emotional disabilities need something far different than children on the Autism Spectrum. Typically, these kids will be serviced in far different programs and in very different ways.
Often an Autism diagnosis is needed to gain access to useful programs like STAR or TEACCH.
That is one consideration, but there are many others. The needs of the child are paramount. If you suspect your child is mislabeled and doesn't have the right fit for a program, it may be time to write out a new request for a re-evaluation. Parents can do this at any time. Though, remember the system is crowded, and the process doesn't happen overnight. Major concerns can be dealt with while the eval is underway.