This is a short guide on how to fix most geometry clipping problems between TF2 player models and items using layer masks.
If you're unfamiliar with layer masks I won't go into detail explaining them here; you should look them up yourself and how exactly they function in an image editing software of your choice. If, on the other hand, you are familiar with them, you probably don't need this guide.
This guide applies only to images/ posters and not videos (though you could repeat this procedure on frame by frame basis, in principle).

The basic procedure goes as follows:

• Render the scene with everything in place
  
• Hide player model(s) whose geometry is clipping through item(s) and re-render the scene again
  
• Add renders as separate layers in an image editing software of your choice. Place the layer(s) containing only item(s) above your base layer (the one where clipping is visible)
  
• Add layer mask(s) on layer(s) containing only item(s) and fill layer mask black, then paint white only over the parts that are clipping

Depending on scene setup, render settings (lights, ssao...) and number of items clipping (and their hierarchy) the procedure to get rid of all geometry clipping problems becomes more complicated (having more layers and layer masks to keep track of models hierarchy, using shades of gray instead of pure white/black on specific parts of layer mask for better blending, manual paintover if all else fails, etc) but this simple masking trick should get you most, if not all the way there.

Although this guide was created with TF2 items in mind specifically, the basic idea should apply to many other models you may experience clipping problems with in SFM.