Is it permissible to dispose of surplus goods and personally benefit from them after the general manager refused to list them in the company's inventories and requested that the matter be handled away from him?

You have done well in seeking to clear yourself of liability. However, the manager's response allowing you to "dispose" of the surplus equipment does not make it permissible for you to take it. The manager is not the rightful owner; rather, the rightful owner is the company's proprietor. The manager's statement that he cannot list it in the inventory does not mean you can take possession of it for yourself. Instead, efforts should be made to include it as part of the company's assets.