Hello Piotr,
Look at this link https://docs.atlassian.com/software/jira/docs/api/REST/7.6.0/#api/2/project-createProject
This is the REST API for Jira 7.6.0. If you look at the schema, there is no way to set the issue type scheme at the project creation, or even to modify it.
You can modify the Issue Type Scheme associated to the project after the project creation, but it is not very practical.
If you are looking for a way to simplify the project creation process, you can take a look at a plugin called Gaia for Jira https://marketplace.atlassian.com/plugins/ca.nuum.gaia/server/overview
This allows you to configure a project template by specifying the schemes (on any type) you want to use for that project type (you even have the option of making a copy of that scheme at project creation, like Jira does). With that plugin, you could configure a Issue Type Scheme the way you want (and add issue types to it the way you were able to with the default issue type scheme), create a project template with Gaia for Jira, and specify your scheme in it. That way, each time you create a project using that template, it will automatically set the correct schemes at the project creation. The plugin also comes with a REST API you can use to create projects by specifying the project name, key and Gaia template you want to use.
I hope this helps.
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