InDesign and Photoshop share the same Bevel and Emboss code, and that faceting you're seeing is just part of what happens with the Chisel bevels (hard or soft) in either program. Bevel is an algorithm, and it imposes a not-always-natural-looking pattern to the "chisel marks," although Hard Chisel produces much less pronounced artifacts than Soft.
To get the effect you're looking for, though, requires more than InDesign can do, so the answer is to use Photoshop.
Apply the bevel in Photoshop, add a layer mask, then use an irregular brush to mask out small areas of the letters, which will appear as "dents" in the letters. Add some dodge and burn or painted overlay to get the shading right.
Even in your Hobbit-inspired example, which was created in Photoshop in just this way, you can see those regular soft chisel marks in the bevel. It's less obvious because it's not being applied to pristine Trajan as you're doing in InDesign.
Applying these kinds of effects in InDesign directly is a fantastic way to add Photoshop effects while still working with InDesign's typographic engine. In most cases it saves time and you get all the advantages of both programs. But there are effects and nuances that still require full Photoshop rather than the "Lite" (or "headless," as John Nack called it) version that was originally built into InDesign CS4.