I think I might have maybe solved it actually, so sorry for the false alarm. Changed the 3 entries to look like:
NukaFactory2,120,36,86,-17,0,burnt_forest/pine_forest/snow/desert/wasteland,city,downtown/industrial,,
Nuka_Factory,120,36,86,-17,0,burnt_forest/pine_forest/snow/desert/wasteland,city,downtown/industrial,,
Old_House01,34,23,29,-2,2,burnt_forest/snow/pine_forest/desert/wasteland,town/city/wilderness/rural,residentialnew/residentialold,,
King Gen still tells me it's skipping line 549 so I just commented it out and edited these to add the missing township values. Thanks for the great mod btw.