Permit locked areas are usually easily be bypassed by dropping down or climbing up to the edges of the galaxy, it's not hard and you don't need a huge jump range, I have done it in a 30ly jump range T6. Just drop down low, select a star directly below you target nebula at the same height you are and off you go. Other methods work, as suggested by Tetra Trash, fly as close as you can to the permit locked area, navigate around it.
The reason the route plotter won't do it is because it is not able to map a large deviation from the direct route, this prevents people waiting sometimes 30 minutes or more as used to happen before this change was made. The galaxy is huge, there are a lot of stars, trying to plot every possible route around a blockage just doesn't work, humans are much better at that than computers.