For anyone who might be interested, I think I might have found something that works. I had to make a small lye solution to strip some average anodising off a not-saber project. On a whim, I decided to dunk one of my deep etching test pieces in it for about 30-45 seconds, and then scrub the etched area with an old toothbrush. And that worked surprisingly well. It smoothed over the rougher spots quite nicely, without damaging the non-etched areas. Here's a before and after:
(https://live.staticflickr.com/65535/48736127481_934d1fe58d_k.jpg)(https://live.staticflickr.com/65535/48735835183_9ebb6d18a4_k.jpg)
Before had a rough feel to it, almost like 120 grit sandpaper. Not nice to touch, definitely on the ugly side. After is still a bit on the rough side, but the feel is closer to 800 grit sandpaper. Much smoother.
I used a mix of 250ml tap water, 50g sodium hydroxide (aka lye, caustic soda, drain unclogger pellets.) Test pieces dunked for 30-45 seconds, then rinsed under running water for 30 seconds, followed by scrubbing with an old toothbrush. Repeat three of four times.