That's not really a bug but, more a side effect of having added multi-liveries support, using the standard method, instead of DirectX 11.
Before the update, there weren't any vehicles which were operator specific in P3D4/5. We only had some blank vehicles with a "base color" and while P3D V4 was then capable to create the operator logo "on the fly" using DirectX 11, in P3D V5 you only had the blank vehicle but, at least, the base color was correct, because there weren't any operator-specific livery combinations, so in V5 you only got the blank generic, but in the right base color which was selected just like P3D V4, but with no DirectX to add the logos.
Now, with multi-liveries back, the generic blank vehicles would only be used in very rare cases, if nothing better is available for an airport but, most of the times, the operator-specific variant will be found so, this variant gets its base color by means of a texture "Fallback" command in the object TEXTURE.CFG file, which instructs the sim should look for a texture in other folders.
Since the WN set of vehicles all have their fallbacks pointing to some "texture.red" folder (exact name changes depending on the vehicle), that's what makes them red, the base color parameter of the rule won't affect its choice anymore so, the only way for you to have a "full_blue" version would be changing all Fallback lines in the TEXTURE.CFG file in the "TEXTURE.WN" folders of all vehicles to read "full_blue" instead of "red".
If you think the full blue livery would be more appropriate for Southwest, we might make that change official, since any of your changes would then be wiped out by an update.