JL-2 probably carries only penetration aids with the 1MT warhead. The same goes for the DF-31/31A. 1MT would level a humongous area. JL-3 would likely be the true MIRVed SLBM. Question is, is it a naval version of the DF-31AG or DF-41?
Since warhead power is more or less directly related to weight as well - it's not even sure the warheads on JL2 is around 1MT range.
If, for example, lowering the warhead to 300 kt can yield 350 kg in weight savings, (modern US warhead weight to yield ratios used) and if such weight savings can result in several hundred km of longer range - i would think the PLA would choose range over yield, in the specific case of JL-2, which seems to be more range challenged than DF-31A.
It'd make sense to use df-41 tech as the basis for jl-3, and use different upper stages. Possibly some parts might be reused but probably all stages and rocket fuel stages would need to be different/smaller. And likely the upper stage would need to be different. Possibly with warheads positioned around the third stage's rocket fuel compartment, as in Trident missiles. One might assume that the current JL-2 configuration is closer to one of Polaris missile, with two rocket motor stages and warhead/decoys sitting on top of the last rocket motor stage, not around it.