The old system has a basic design flaw that way too many build settings come with pike and don't work where the module is compiled. As I understand it, that's difficult to fix in the old framework.
On the basic technical level it's clear how it should work: Settings that affect the ABI (some CFLAGS, a number of macros in machine.h, etc) should come with pike, but not anything else. There's really no room for choice as a matter of policy. Then how to get there is a different matter. I seriously doubt the new system works correctly in this perspective either, because that'd require a deep split of machine.h - it contains both many ABI-defining macros and many configure test results. I haven't seen any hint of that getting sorted out, but I can confess that my knowledge of the external module building stuff is hazy.
