Yes, you can send the 220V straight to a 220v-only panel, but you will need to have a main breaker on it sized appropriately.
Truthfully, the autotransformers do nothing to the 220V loads when connected anyway, other than supply a convenient 100A breaker. But there are some advantages to directly wiring the 220V to a dedicated panel. Your 220V loads will still work fine if the AT fails or its breaker trips. This panel must be properly labeled “220V only” because if someone later thinks ground is neutral and can put in a 120V breaker, the current will go through the ground wire.
Even though you have not included a neutral on the input side, that neutral is still bonded to the ground line at the source of shore power presumably. If you bond the autotransformer neutral to ground in the 120v panel, you have effectively connected the AT neutral and the shore power neutral through the ground wiring. Objectionable current will flow through the ground line. Frustrating, isn’t it?
If you don’t bond the autotransformer neutral to the panel, then you have a safety issue when not running on shore power. I guess I would use the ground relay in the AT as it is designed for this case when running from inverter only, and not hardwire bond the neutral to ground in the 120v panel.
This solution does not address the potential mismatch of voltage between the AT neutral and the ground when running in shore power mode, and I’m not sure if that will be a hazard or not.
I have no experience with two ATs in the same system, so I can’t comment there. In principle, they can be wired in parallel to increase available neutral current.