LayereLayout looks for the longest path in the graph, and assigns the graph layers relatively to that path. TimeLimit limits only the time the path-finding function is allowed to run. In your case the longest path is of length 1 and is found immediately, so TimeLimit doesn’t have any effect.

This version of the flowchart.dll adds a SwapPairsIterations property to LayeredLayout:
https://mindfusion.org/_temp/FlowChartPro.zip

Setting SwapPairsIterations to 0 should make LayeredLayout finish in less than 20 seconds, but without trying to untangle crossing links. You can assign to the new property values from 0 to 5, which let you control how much time is spent for decreasing link crossings.

RouteAllArrows will work faster if you set a larger RoutingOptions.GridSize. You can gain better performance if you re-route only the arrows that are not processed by TreeLayout, e.g. ones that go up in the tree or ones that merge tree branches at some node.

I hope that helps,
Stoyan