OP is evidently talking about this sample, and modifying the IdentifyParameters. The behavior appears to be related to the new MapImageLayer highlight feature of 4.25.
It appears there's an expectation that setting returnGeometry to true will automatically highlight the feature on the map, but the API has never worked this way. One must manually create a symbol and add the graphic to MapView.graphics or something similar.
However, OP has noticed that when specifying returnGeometry and sublayers, the feature does get highlighted (new to 4.25). Under the hood, the identify operation retrieves the features as graphic objects (as expected), but when sublayers is specified within the IdentifyParameters, the operation sets an undocumented property called "sourceLayer" on each returned graphic with the related Sublayer object associated with that graphic's layer. The graphic having this sourceLayer property specified is what triggers the highlight when the graphic is added to the Popup.
This can be demonstrated by adding the following line immediately above original line 148 (return feature):
feature.sourceLayer = identifyLayer.sublayers.getItemAt(result.layerId);
...and the following line above original line 80:
params.returnGeometry = true;
The subsequent highlight operation causes the additional query request. I would agree with OP in that the query is unnecessary since the geometry already exists on the client, but it is what it is. Regardless, though, the query is often worse that it looks. It should only retrieve the specified feature by its objectID value, but it seems more often than not, it doesn't include the objectID in the request, and therefore requests all features in the layer (see attachment)...which is really bad.
I've also seen the additional calls to export mentioned by the OP, but it seems kind of sporadic (not in the attachment for that run), but never actually does anything useful when it does execute.