The patches restrict local uploads on mediawiki.org (T217523). There were no errors during scap deployment, just the local uploads were not disabled after deployment.
Yesterday, I've merged 494218 and pulled it to mwdebug1002, but it did not work, so I've reverted it with 494707.
Today, I've merged 494806 and pulled it to mwdebug1002, but it did not work again. I didn't think it would break anything so I've done a full deployment. It didn't work even then.
I've decided to deploy a patch that was next in SWAT calendar (494225) that changes wmf-config/InitialiseSettings.php and see if then 494806 (dblists/commonsuploads.dblist) would work. To my surprise, 494806 (dblists/commonsuploads.dblist) worked after 494225 (wmf-config/InitialiseSettings.php) was deployed.
I'm not sure if that's a bug in Scap.