Glad it worked! Yes, this solution is a little cumbersome, sorry... making this easier is on my radar 
One workaround is -- once you've got a palette you know you like for a set of boxplots -- downloading the specification for each boxplot, and then using a script to automatically apply that palette to each of the boxplots' specifications. This reduces some of the hands-on work, hopefully (esp if you have like 10 boxplots of the same data but different log-ratios).
If you're not comfortable with programming that may be more work than it's worth, but if you feel like giving it a shot we did something similar for our paper here (see biggify.py for an example of auto-modifying Vega-Lite specs).