You can read up on numerical diffusion here. I think adding boundary layers won't help much. As you are trying to capture recirculation zones, you'd be better off using structured hexa mesh for your model. You can decompose the domain into multiple blocks and obtain it. You can also try an axis-symmetric case (if it's applicable for your geometry) before moving on to 3d periodic. Also, you'll find more similar numerical modeling work in journals (use keywords like "gas atomizer, atomization nozzle") to get an idea of how people approach this kind of problem.
Can also check out this flow in a nozzle on Ansys Innovation Courses (open source) and transient flow (this one uses poly mesh). Not sure if it'll help for your geometry, but check it out anyway.
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