In #145, all carriable containers are disallowed to stored in the seat inventory. However, this should not be the case for cardboard boxes. Since they can be packed into only 3 litres, it is more reasonable to allow storing them in the seats.

Consider after landing somewhere, a kerbonaut may need to EVA carrying a bunch of items stored in the seat together with some parts removed from the vessel (so that they can't carry them in once without a box). It would be more reasonable to take a cardboard box to fill everything else in.

With #145, we have to use an additional container part for the cardboard box, which is especially unfeasible early in the tech tree. No container part fits well for early 1.25m landing/re-entry command pod, either too big (IMiC-800) or would significantly tilt the center-of-mass (storage lockers). Another way is to attach an empty cardboard box to the top of the pod. This is way too ugly.

It's a limitation of the current implementation. Any carriable item immediately equips when stored into a personal inventory. For this reason only one carriable item per personal inventory is allowed. Seat inventory is just a reflection of kerbal's personal inventory, so all the same limitations apply. In the editor the seat inventories are available only to fill the kerbal's inventories.