He is running his show as if he supports Trump and that’s all Trump cares about. It’s not that 1 literal vote from Joe. His disproportionate Trump coverage (practically obsession) and resulting free publicity has paid off for Trump many times over.
He and Trump (and Mika) are longtime friends so I’m pretty sure this ‘non voting’ disclaimer is for the primaries when it won’t matter anyway. Joe and MSNBC are probably particularly sensitive to his credibility after having called himself a supporter the other day.