There is a topic with the same title on reddit.

https://www.reddit.com/r/Houdini/comments/ul0uk3/how_to_model_muscles_and_avoid_intersection/ [www.reddit.com]

I wanted to throw my two cents in the hat, and figured I do it here so I could include a hip file.
If anyone else has suggestions(or criticisms) feel free to throw them up here.

My method involves using SDF's to solve the penetrations between intersecting muscles. This way you can model your muscles(in houdini or elsewhere) without worrying about inter penetrations until afterwards. I done it manually one muscles at time, but I'm sure if you are clever you could do it in a for loop.