The fade in/out works perfectly if stationary in a single biome based off of the time of day, however if you have a setup that involves various sky textures for different biomes it introduces a jarring pop in and out effect each time you cross into a new biome. Is there a way to address this that does not involve editing tons of configuration files for each new sky instance?

Have you tried the transition speed variable in the default properties object? https://github.com/AMereBagatelle/fabricskyboxes/blob/1.17.x-dev/docs/schema-v2.md#default-properties-object
There is no way to fix it without editing each configuration file.

Closing, for desired effect transition speed should be <0.1 to more slowly fade in/out.