This is still an issue in Tableau Prep 2018.3
The issue is not one of how to re-arrange the columns in the flow file, that is simple as you have shown. Once you have defined a column order, if you run the flow from the command line (rather than from within Tableau Prep), then the defined column order is ignored.
I've just been experiencing the same issue. Command Line execution of Prep does not show specific column order.
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I raised this as a bug with Tableau Support and have received the following response
"Thank you for your patience while this case was in our Resolution Queue. My name is Laura and I will be providing further assistance with this Support case.
I investigated the issue and located an internal open issue that matches the reported behaviour. The internal issue is currently under investigation and is identified by number 820196.
When a resolution for this issue will be incorporated in a future release, it will be included in our release notes for that specific release with the Issue ID number provided above.
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Hello, Many thanks for your update.
My Project has to find a workaround to execute the flow file.
Unfortunately, It seems that the software quality of the Prep does not better than I thought.
I hope the bug would be fixed soon.