When I change the CPU Speed in the Tools menu I would expect that some of the MCG registers would be changed.

Once I compile I do a Export compiled Binary.

However, when I flash the chip from my J-Link and subsequently examine the memory using J-Mem I was expecting to see MCG_C2 and/or MCG_C5 change, but they don't.

I always get the same values from 0x4006 4000 - 0x4006 400D:

MCG_C1 0x20
MCG_C2 0x24
MCG_C3 0x6A
MCG_C4 0x0B
MCG_C5 0x40
MCG_C6 0x40

MCG_S 0x6E
MCG_SC 0x02
MCG_C7 0x00
MCG_C8 0x80

Does the Teensyduino program only change the clock registers when downloading through the Halfkay download and otherwise (when exporting the binary) use what is in the files mk20dx128.c and kinetis.h?