I have a similar problem. I use the same workflow as you, but Media Encoder is putting out 49Gb file, even though I’ve set the bit rate to output a 20GB file, whici is way to big for my 25Gb disks. I can’t figure out why this happens. I have an encode going on right now, but am using the “Blu-Ray MPG2” preset. I hope that works.
BTW, the “extra” Gb’s in your build may be because of the audio file. I always use Dolby Digital, whic produces much smaller file sizes. Juat a thought