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Good Morning Stuart,
Good questions and observations.
You've described the primary pros and cons of using the command line over the UI Sync client pretty thoroughly. One item, the command line not only provides refreshes but can also allow you to append to an existing published extract, should you require that option.
In regards to the question 'Should we switch'? As we say in Texas, 'if it ain't broke, don't fix it'. It sounds like you have an excellent handle on how the refresh process occurs and the command line approach gives you a little more control over the process.
I'm happy to hear other's thoughts on this.
As far as Gremlins... That would take some diagnosis, it could include network issues outside Tableau Online, issues at the source being refreshed, etc. If it persists or worsens, please open a support ticket.
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Tableau Online Deployment Advisor