Short answer is yes you can, long answer is you’ll have to create a custom profile, depending on what you’re using handbrake or ffmpeg you’ll have to write up the custom commands for those encoders, there are many different ways to do it so each encoder community would be the best bet. Make sure you’ve set the encoder optimized flags in your profile (see Advanced Commands <encoder>-VideoOptimized=true) so that MCEBuddy doesn’t “overwrite” your settings with it’s own logic.
E.g with ffmpeg you can use -vf scale or -vf setsar or combine them based in input width -vf scale=iw*55:ih,setsar=1:1 etc. You’ll have to decide what’s best for you, scale, SAR or PAR.