Hello!
In the latest runtimes, Spine's scale mixing is implemented such that the destination scale sign is applied immediately, instead of having it scale from -1 to 1 naively. This is because people use negative scale to flip bones between animations but never intend them to flip like paper mario does.
If that was the effect you were going for, it is actually just a matter of removing a block of code in the ScaleTimeline type that favors the destination animation's scale signs.
But Yoyo Games actually manages and maintains their own version of the Spine runtime that's out of our control. And from what I understand, it's precompiled and not user accessible. So there's actually no way to resolve this that way in GameMaker specifically.
So yeah. The way to do it is probably to make those actual custom transition animations rather than relying on Spine's automatic mixing. Or code the scale transition manually instead of relying on Spine animation mixing to do it for you.