AROS is an API clone of Amiga OS 3.1, identified in the Agreement as 'The Software'. Amiga Inc are prohibited from selling anything running a substantially similar software architecture, either by themselves or through licensees. This includes any substantially similar software, not just one developed by Amiga Inc. No doubt Hyperion would have had MorphOS and AROS in mind when they negotiated this aspect of the agreement.
AROS being open source and free of charge is irrelevant. The agreement clearly states that the Amiga Parties will not distribute, free of charge or otherwise, any software exhibiting a Software Architecture (note - software architecture, not CPU Instruction Set Architecture) similar to the original Software.
Regardless, CommodoreUSA's attempt to use AROS as a link to the classic Amiga depends on AROS being perceived as substantially similar to the Amiga OS. Whether or not it is, they think it is and so have exhibited a worrying lack of regard for the Legal Settlement. Assuming of course that Amiga Inc have actually licensed the name, since we haven't actually heard any kind of bilateral acknowledgement of this, or any third party source supporting it.
Of course, CommodoreUSA could simply decide not to bundle AROS, but their PCs really rather depend on having a substantial link back to the original Amiga lineup. In my opinion, running AROS isn't nearly enough, but not running AROS out of the box would be worse.
Basically, if Mr Altman wants to make money, he would be better advised to stick to the Commodore brand and make his money from the nostalgia for the C=64 for now. In the highly unlikely event of this being a success, he could then move onto the Amiga scene with the aid of some PC-64 derived profits, but as it stands the legal situation is too much of a minefield. Why expose a fragile startup to unnecessary risk?