When I made a character for Dark Heresy (many moons ago) I believe that the starting skills listed with the career path were all considered 'trained'. This idea was reinforced by the fact that they weren't listed in the Rank 1 advances. So, when I started making my new character for Rogue Trader, I expected the same thing. But, most of the starting skills are also listed in the advances for Rank 1. I'm not sure why they would be listed there if the character gets them for free, unless they're there for characters coming in from DH.
Anyway, I couldn't find anything that explicitly stated that "new characters are considered trained in their starting skills".
Best Answer
They are in fact at trained. The reason for them being listed in rank 1 is for variant character types and origins; it's quite possible a GM might let you swap one for a different skill of the same value. Also, as you noticed, DH characters can be crossed into those careers.