To me, this goes far beyond what I would consider a feature. Instead, it creates confusion, wastes time, and makes the UI behave in a way that is difficult to reason about.
I recently discovered that whether secondary branches in a stack are shown or hidden depends on which PR happens to be selected in the UI. What I find particularly problematic is not the behavior itself, but the fact that there is no obvious indication that information is being intentionally hidden. As a result, I spent an entire afternoon trying to understand what was happening, assuming I was dealing with a bug, a corrupted stack, or some synchronization issue. Only by chance did I eventually discover that this was expected behavior.
I struggle to see the value of hiding branches without providing a clear and prominent indication that the view is being filtered. From a user's perspective, hidden information is often indistinguishable from missing information, and that naturally leads people to believe something is broken.
I would strongly encourage you either to remove this behavior or, at the very least, make it unmistakably clear in the UI whenever branches are being intentionally hidden. Users should never have to solve a puzzle to understand why information they expect to see is not there.
Developers rely heavily on these views to understand the state of their work. Time spent reverse-engineering UI behavior is time not spent reviewing code, fixing bugs, or delivering value. In situations like this, predictability and transparency are far more important than clever filtering.
My general feedback is simple: please do not hide information by default, especially without clearly communicating that it is being hidden. The screenshots below illustrate the issue far better than words can.
I realize my frustration is evident in this message, but it comes from having lost a significant amount of time investigating what appeared to be a problem that ultimately turned out to be an undocumented (as far as I know) UI behavior.