Is there a way to override texture compression format for a WebGL build target per platform? Like iOS will use RGB Compressed PVRTC 4 bits, Android RGB Compressed ETC, desktop RGB Compressed DXT1, etc. Or should I use some editor script that will modify all of my textures, build and then repeat for another platform?
You mean the setting in the build settings that can be done as profiles and per target?
Player Settings contains platform-specific settings.
For WebGL and textures specifically I believe the manual recommends creating a custom build script in order to toggle additional settings for mobile vs web builds. If I recall correctly that was maybe 2-3 lines of code in the method body. Check the WebGL platform section.