We do not change shaders assigned at materials, however there might be circumstances where materials are assigned, which might implicitly lead to a changed shader.
We need more context information on your setup, such as the Spine components used on all your GameObject nodes of the character, e.g. if a SkeletonPartsRenderer is used, or only SkeletonAnimation components, etc.
I guess it is not possible for you to set the material's shader in the Unity editor instead of via code - this would perhaps be the easiest solution.
In general it would be best if you could create a minimal version of you project that still shows your problem and send a zipped package to contact@esotericsoftware.com, then we can have a look at it.