MSPM0L1106: Why do I get a warning when uncheck the Sysconfig option for linker file generation

While migrating our project to SDK v1.20.01.06 I discovered that Sysconfig now automatically references a linker command file and startup files from the SDK. While I can see the benefit of this for migration between devices, we need a custom linker command file that we maintain. When I uncheck the Sysconfig option to do this (option 2.1 described here) I get a warning within SysConfig (see below). Why should I get this warning if custom linker command file is a valid option? I feel that this warning creates undue concern and confusion. What is the purpose of this warning.