It would be interesting to know how South West gets around the issue of trim as they have a very liberal seating policy. Unless things have changed recently they allow passengers to seat themselves - a "first in, best seated" policy if you like. No doubt they've found a happy medium between buffering the CG envelope and allowing flexibility in seating.
On the issue of lateral imbalance, the 762ER, 763ER and 744 aircraft all have lateral imbalance limits. For the most part the limits only apply when operating in a very small region of the CG envelope near the MTOW. The region can be so small in fact that some operators choose to exclude it from the envelope altogether, and forgo any issues associated with having to consider it.
If operating in the lateral imbalance region of the envelope and the lateral imbalance limit is exceeded, there is a variable weight penalty applied to the maximum taxi weight. The limit itself isn't imposed for aerodynamic reasons but rather for taxiing reasons - and hence the penalty to taxi weight and not take-off weight. My understanding is that FAR25 aircraft are certified to fly with one wing tank full of fuel and the other empty. Any lateral imbalance due to loading would be insignificant compared to the above ... one would have thought.