Gaius Magnus and the irradiated legionnaires appear and I jsut wiped them out

But I haven't even started Lonesome Road...

any reason why this may be? I did use TMM 1 so if the location doesn't exist until after wards normally then that explains it.

Yes the location is unavailable until after Lonesome Road (depending on your choice at the end of the DLC). Gaius Magnus is always there, you just can't usually access the area.

Te locations appear as soon as you download the DLC, but like Vexen said, access is usually denied until after the DLC.