Yes, the "dynamic" layout mode ignores the default coordinates. My best guess is that you could try to start the NetChart in "static" layout mode which does respect the default coordinates, and then switch to "dynamic". I think that should bypass the "randomize new node positions" phase in the dynamic layout, but you'll need to test to make sure.
As for detecting this automatically - yes, I think we should do that. I'll add this feature request, but I don't know how soon we'll make it (likely sometime within the next 6 months).
For different layout algorithms (hierarchial, radial) - yes, they are centered around some "starting" node and fail in these cases. Fixing that is already on the TODO list, though, again, I don't know how soon I'll get to making it.
Btw - the "starting" node used to be the "last focused node", but this got broken in 1.10. Now it's just the "first node", but I'm in the process of fixing that. I believe the fix should appear in 1.12.