What Harald said applies to data export (JSON and binary), but I realize you are only concerned with the texture packer output, even though you are also exporting data. Note you can also run the packer separately if you like, without exporting data. To get < 4.0 compatible output, check
Legacy output. When exporting data < 4.0, the packer pretends this was checked, even if it wasn't.
I see the differences you explained. We've fixed the problem in 4.0.46. Sorry for the wait!