The hudson.model.Run.ArtifactList.treeCutoff property does not merely affect the manner of listing artifacts on the Job's HTML page, but also limits the number of items retrieved by the API. You can confirm this by polling <hudson>/job/<jobName>/<buildNumber>/api/xml?xpath=//artifact with different settings for hudson.model.Run.ArtifactList.treeCutoff, and as long as you actually have more artifacts than the treeCutoff, the number of items found will always be only one more than the value of treeCutoff.

The UI configuration parameter should not affect the API results in this manner.