I decided to replay Battletech now that two of the dlc's are out and was wondering if they activate during the story campaign or only after/ or in Career mode? With flashpoint I found that if I used the same character from the main game the new mechs were already obsolete or under tunned.

I would go for new Career mode. As all new mechs are lights and also new FP seem to be for sooner in carrer. I also do not beleive the FP are showing during the campaign.

But you will lot of Javelin everywhere so that is a plus :D

Yes they are in the stroy campaign.