Chain is applied after the DoTs to make it align with the rest of the raid buffs, like Trick Attack, Embolden, etc. Same reason why most raiding RDMs will use Embolden way before they get enough Manas to do their combo burst.
That said, if you're going purely for personal gain, use Chain before your DoTs, particularly before you Bane. I'm not 100% sure, but my assumption is that DoTs will snapshot not having Chain on the target if you use them before.
