If this was the case, then why was Hot Toys unable to produce Aliens marines with reasonable likenesses? Same for the first Arnold Terminator? What about Kane from Alien? Actor likenesses have to be approved by actors before figures can be made, unless the contract they signed for merchandising allows for the use of their likeness. In the Matrix case, I suspect Keanu signed away likeness claims, seeing as how toys and video games were made from that franchise. But whether that was the case or wasn't, the movie studio (and Keanu) has a right to make money off of his likeness when portrayed as a character from that film.
Here's an example of a lawsuit regarding Arnold and a bobblehead figure:
https://www.nytimes.com/2004/05/18/national/18arnold.html
The Matrix figure exhibits precisely the same problems that this new Metal Gear figure does.
HT may be able to get away with the nude bodies because they don't obviously represent versions of that actor or actress from film or TV show X. But if they're gonna go after another company in the way they went after Headplay, then that smells of hypocrisy in this sense, as well, since HT is skirting the payment of rights to actors by sticking their heads on nude bodies.
Small time customizers usually act with impunity because they have such a small, niche market that it doesn't affect anything in the grand scheme of things. That's why the mass produced component of this figure distinguishes it from, say, a customizer making 10 Snake figures.
. But, I don't believe that it's fair to liken the Matrix and the "Metal Boss" figures in the same way, or accuse Hot Toys of being hypocritical in this. Like you said, Keanu Reeves had most likely signed off his likeness rights for free use. However, in the case with the "Metal Boss" figure, Yoji Shinkawa and Konami did not give their consent for that character to be used commercially without their approval. The fact remains, that Hot Toys had to pay a licensing fee, and get the permission to make Metal Gear Solid figures, while Headplay simply ignored that process and went full-steam to mass produce his own bootleg Snake under another name (Metal Boss). 
My Metal boss will be arriving next week!!
