I'll write right away that I have no experience with Unity. I am only expressing my assumptions, so you should not expect much from me.
JulianRice yazdıDo you mean not selecting Premultiply Alpha in the settings?
JulianRice yazdıis there an alternative to re-exporting every single SPINE project with this single checkmark toggled off?
I assumed the problem was with this checkbox in import/export.
In Spine Web Player we have "premultipliedAlpha" parameter with "true" default value. This parameter and its value are used in conjunction with "Premultiply Alpha" in export settings from Spine. As I understand it, if the checkbox "Premultiply Alpha" was checked during export from Spine, then we must set "premultipliedAlpha" = true in Spine Web Player.
Maybe same for Unity? Maybe somewhere we have something like "premultipliedAlpha" too? And you don't need re-export all yours spine projects?
JulianRice yazdıHowever, some of the pieces (layers I assume) seemed a bit blockier, and there were some bits of white/transparency that appeared for the first time as a result. Do you have any idea what this could be?
No idea. Although I sometimes got strange graphical artifacts in Web Spine Player due to strong discrepancies in versions. My json-files was generated in old Spine Editor. Looked for discrepancies in formats, corrected files.
But for Unity, are there separate runtimes for each separate version of Spine?
Btw, I see this yours "bits" in picture in first post too.
Can you check this model in Spine Editor? Maybe this is not problem with Unity, but something with model?