Agreed, it is clear you help win a great victory for a battle on Corellia from the planet story as the Empire but it is made very clear that the Empire eventually loses the war(for Corellia), despite that battle. You also have to remember that the stories on corellia, while going on around the same tie are not actually simultaneous. They do happen in an order which you have to piece together.
For taris/balmora I think at least a 6monthes - year has passed by the time chapter 2 happens, I always found this also very clear that they were set in different parts of the timeline and had no issues. HOWEVER, I will say the 8 class stories are fairly interwoven in references so if you've only played one class it may be harder to piece together a lot of the chronology on ANY planet.