It may be a newer interface mishap actually. Kept arguing with it as well. 
No need for the delay. Just fix the hitboxes for the navigation sidebar and hierarchical pop-up - does it have a name?- (no triggering unless we poke them specifically) & fix the position of the space we write in and its controls if need be (the writing zone + controls can be moved right slightly, if necessary).
For the sidebar, just give it a slightly shorter trigger, it should be fine. The pop-up lines and nodes thing can have a small button hover trigger up near the … menu button, no need for it to hang over. The buttons and hitboxes for the … and X node thing can be reduced to the size of the < > arrows found in the App.
Consistency also helps visually 
Issue examples:
If you come up from a bit under the Rem, you have more chances to not trigger things ATM, but in some situations, stuff simply overlaps and you can’t scroll the issue away…
Sometimes we get an arrow, instead of triggering the pop-up, albeit we aren’t usually that lucky:
Pretty sure that folder’s (M3 Mechanism) arrow isn’t anywhere near the common sense trigger point, yet the pop-up triggers even at that significant distance from the top of the page:
