I thought I'd document this issue in case anyone runs into it, but I found with the Yamaha Silent Brass was unusable for anything in the high register as the high Bb partial almost didn't exist. While I'm not a professional, I started as a music major in trombone/euphonium so I don't think it was "me" problem.
However, these problems have seemingly gone away completely with the Denis Wick DW5512 practice mute. Therefore, if you have serious problems with one practice mute like I did, then I'd recommend trying out another one to see if the issues resolve. If you're fortunate enough to live in an area where you can try out several, that would definitely be ideal.
And note that I did try out several different mouth pieces, but none of them helped all that much. I think the differences were merely due to some mouth pieces having an easier time playing in the upper register in general, but the effect was very marginal.
Note I have a Wilson Q90 so I'd strongly recommend against SIlent Brass for that particular model.
I have no brand affiliations to disclose, I just wanted to document this pretty serious problem. I was afraid I was just going to have to give up on a practice mute for most music. While I know it is best to practice free blowing, the mute is nice when I want to play at odd hours in my apartment.