Ok so i managed to figure it out, it seems you need to use the off mesh tool to tell the pathfinder to use the right path for broken meshes.
For anyone interested in a fix, you can paste this in the OffMeshConnections.xml with the bot off
<OffMeshConnection>
<Path>
<Vector3 X="-9014.484" Y="872.5606" Z="148.6167" />
<Vector3 X="-9021.027" Y="890.2583" Z="29.62078" />
</Path>
<ContinentId>0</ContinentId>
<Type>Bidirectional</Type>
<TryToUseEvenIfCanFindPathSuccess>true</TryToUseEvenIfCanFindPathSuccess>
<Name>Mage Quarter</Name>
</OffMeshConnection>
I've tested it a bit, seems to work mostly ok, it might need a bit more refinement but ideally these should already be included with the bot on download, kinda silly to browse through years old of forum threads for half baked answers and poor documentation.
flaw0flife got a reaction from Droidz in Stormwind mage tower pathfinder broken