Sorry for the late reply but this is sort of my own little story that kind of deviates from the main Xenogears plot. This happens quite some time after Elly and the crew gets caught in Solaris and thus Elly is taken prisoner and made to breed and give birth to Deus.
Other than fetish reasons,the reason why she is well muscled is because one of the experiments Elly goes through turns her usual modest petit frame into something that can withstand the rough breeding sessions with specifically engineered Wels that will impregnante Elly as she eventually gives birth to Deus.
As you can see,Miang is enjoying things and Krelian cannot bear to look at Elly and leaves the room. And this is just the tip of the iceberg.