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If he has authority to bind both companies with his signature, then he can sign the document on behalf of both companies. Ultimately, the companies would have recourse against him if he is entering into the agreements against the welfare of the companies and in his own best interests. However, what he is doing is legal.
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As long as he has signing authority, he can enter both companies into the agreement, independent of the nature of the entity. This means that even if a corporation is a not-for-profit, if he has authority, he can bind it to a contract.
If he entered into the contract and it was not in the best interests of the companies, the companies' boards of directors and/or shareholders may be able to hold him responsible for the decision.