Hello! We already added to our tracker your suggestion for bone scale:
Bone scale per project · #542 · EsotericSoftware/spine-editor

Export settings per project are already available, just save after exporting. We are also planning to add the ability to have them relative to the project:
Allow export paths relative to the spine project file location · #515 · EsotericSoftware/spine-editor

It's been around since 3.6.16:
Problems with exoprt settings in the last Spine update
[Request] Remember last folder exported to from this file

Remember to save AFTER exporting and not before!