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There are quite a few SQL queries that don't work in Alteryx, just as most Alteryx-formed SQL queries don't work in SSMS. Order by is one of said queries. I have only begun using In-DB tools as well
If you are looking to sort your data, you'd have to configure your Sample In-DB like shown below. You want to change the top left box to Percent and type in 100 and tick the "Sample records based on order:" box.
Otherwise you'd have to stream your data out and use the normal Alteryx sort tool.
I have noticed that sometimes the Sample In-DB doesn't work as intended for me but the majority of the time it does. Haven't been able to work it out yet though.