I have notice this when you select some of the predefined project templates. For example, if you select the "Agile Scrum" option when you create the project, a simplified workflow is created for the project.
I don't like it and so I usually create a project using jIRA classic option. After creating, you will have to change the schemes to associate the project with predefined workflows if you have any.
The other option is to create a project blue print and use it while creating project. You need to write a plugin for that.
I use this approach A LOT and it works wonderfully. It even allows you to copy issues, versions, and components if you want to configure your template to that level...
You can also copy a live project's configuration to a new project if you just need to knock it out quickly... just make sure when copying the project you don't copy issues as well.
You could look at some of the plugins available on the marketplace (disclaimer: we're one of them - https://marketplace.atlassian.com/plugins/com.wittified.jira.project-creator) which allows you create customized templates for your specific purpose.
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