There is no actual reason for it being limited to 64k. For the public instance/class structs the 64k limit exists because of the limitations of GTypeInfo but there is no such limitation here.
As in various places we sum up all the private struct sizes and still require the sum to be smaller than 64k, it can relatively easily happen that some type is hitting the limit. As this can also happen for example when adding a private field to some base class, which then breaks a subclass that happens to use just too much data now, this means adding private fields can cause ABI breakage.