When I add a feature layer, with many layers, from arcgis server not federated in a map viewer beta, pop-up are not enabled by default.
I create a new item from a URL before adding it in map. All features layers are added in a group (great idea !) but I have to configure pop-ups to disabled and after enabled pop-up on each layer. I tried with a feature layer with only one layer and it works, layer are not load in a group.
On Firefox (68.9.0esr (64 bits)), if I move layers out of the group and I disable / enable on a layer, all layers have pop-ups enabled. It does not work on Chrome.