There are three distinct ways to use the autotransformer.
Step-up, step-down, and balancing.
In step-up (120 to 240V only), you can put up to 28A continuously into the Neutral and L1, and get out 14A at 240V.
In step-up producing split-phase 120/240V, the neutral is both an input and an output. The 100A version will let you pass much more current through on L1, as there is a direct path that does not go through the coil.You won’t get more than 14A out of L2 however.
In step-down (240 to 120 only), you are limited to 28A at 120v continuously (14A at 240v).
If you are doing step-down 240v to split phase 120/240v, the 100A version lets you pass much more current through at 240V as there is a direct path that does not go through the coil. The L1/L2 imbalance still must have less than 28A continuously on the neutral.
Balancing is similar to step-down split-phase, but the input neutral is not connected to the AT. It is critical that stacked 120v inverters have their neutrals connected together, however.
Generator balancing just does not connect the Neutral.
Also, see