Hedgehog Development, the guys that makes TDS has fixed this issue in the next release, presumable v188.8.131.52 which I also tested. Thank you for the superb support!
Make sure to set
filterItem="false" on you site if you need to add or sync a __Standard Values item that has workflow settings with TDS (Team Development for Sitecore).
Today I worked on solution that uses "Live Mode" locally using these settings:
<site name="website" database="master" filterItems="true" enableWorkflow="true" ... />
The template in question was a just "marker" template with no fields but it defined which workflow and which state should be used by future items of that template.
So I wanted to add that template and its the __Standard Values item to my TDS project (using latest version of TDS) but when I used the "Get Sitecore Items" dialog the __Standard values item was not visible from the list of items...
I was a bit puzzled at first and could not find the reason for why this was not working as expected. Since my TDS project was configured to use the master database, and I thought that the TDS connector was running in shell context and would then not be affected of any setting on the "website" site configuration.
Then a good college of mine (Thanks Jesper) pointed me in the right direction to simple set
filterItems="false" and to my surprise it worked!