I just found out, how to exclude specific "spatial relationship layers" from the list in the Query widget.
You can add an array of Layer ids to the following variable in "PATH TO YOURAPP#\widgets\Query\TaskSettings.js" currently on line 459
var ignoredFeaturelayerIds = ;
Here's how to get the layer ids: How do I get the ID of a web map layer?
It's a bit tedious to list them all, especially in case you only want to display one layer and your map contains dozens.
So I was wondering if there is an "easy" solution to:
a) set a default layer to be displayed automatically when "Only return features that have a spatial relationship with features in another layer" is selected
b) instead of ignoring, adding layers
What do you think, would this be worth an enhancement request ?