Keeping body from poking through clothes/armor is hard. Even in Witcher 3 many armors and clothes have this, for example, a belt sinking into nilfgaardian armor when doing certain animations / elf lady’s legs going through skirt when sitting / etc. In my case, i just try to weight paint every ‘layer’ very similar, so this way you can minimize these intersections. Unfortunately I don’t know about any other method than weight painting, which is a pain.