IndieDoroid What does Reference to the meshfilter of other components being lost mean?

It means that if other components store a reference (i.e. have the reference serialized) to the skeleton's MeshFilter, it will be lost. That's because the MeshFilter is not serialized when this feature is enabled.

IndieDoroid If we enable this feature, what are the chances the general Spine user will lose references to the meshfilter of other components?

What do you mean by "the general Spine user", and what by "of other components"? As mentioned above, the MeshFilter component of skeleton GameObjects (SkeletonRenderer and subclasses thereof) are no longer serialized. References to these MeshFilters are then lost. MeshFilters at other GameObjects are unaffected of course.

IndieDoroid I don't think I've done anything special to store a reference to any of my skeleton meshfilters?

If you didn't write code (or use thirdparty code) where you have public MeshFilter or [SerializeField] protected/private MeshFilter members that store such a reference, then you don't have anything to worry. If you don't remember all your code, as no-one does, just use the search function of your text editor.

If you don't feel capable of searching through a lot of thirdparty code, then don't enable this feature to be on the safe side.

IndieDoroid I've been using the RenderExistingMesh for outline effects. Would this be a case where references to the meshfilter of other components, be lost?

If you look at the source code of RenderExistingMesh, it holds a serialized reference to MeshRenderer. There is no serialized reference to MeshFilter.

IndieDoroid Sorry, my technical knowledge is not at the level of a coder

Sorry to hear that. If you take over decisions which require programming knowledge, you should either learn these skills or hand them over to the programmer on your project, or get one on your project in case you don't have one yet.

Otherwise it's a bit like performing tasks of an electrician without knowing which wire stands for what. Wrong wire connections may work out of luck, but the system may fall apart when the project grows.