The "make a salad" example is an exception to the above but I think it gets away with it because the branched paths are of equal length and overall it's not too large. Once you get even slightly off this, like the Mars example where a branch is 1 box longer than the other, it can easily fall apart. Such branching and reconnecting topologies tend to result in things in the editor moving around on you a lot while you're trying to create the paths which can be disorienting as well. Other options such as code2flow which have already been mentioned here can get away with as much on the fly restructuring as they want because they separate graph construction and graph representation in the UI whereas this combines them. Maybe an option here would be a toggle to disable overall graph auto-layout but keeping the keyboard shortcuts and auto default placements? Or maybe it's just best to focus on where it's unique.
An "easy win" feature add for knotend might be a set of shortcuts to change the symbol and maybe some automatic ones like terminals or decisions that get set based on their connectivity in the drawing (unless otherwise manually set). As it is now everything is a rectangle which typically means "process" in flowcharts.