What? o_o. atmelsam is a platform and if you want to switch to a different platform verison, you’re supposed to be using platform = atmelsam@<version>, not platform_packages. (docs, docs). Use platform_packages to control the version of packages, such as the framework-arduino-xxx, as is dispalyed at the start of the compilation. The post contains here more info about this.
Did you report this issue in in the core? Also I presume if you are using an Adafruit board, only the Adafruit SAMD boards core version matters, not the one of the core provided by the Arduino team. Please open an issue in GitHub - adafruit/ArduinoCore-samd if that’s the core you’re using.