Hi glovisol,
I downloaded both your 50Hz & 100Hz sketches, but they do not compile & stop here:
I just rechecked the code on my Arduino Zero using Arduino.cc's IDE, version 1.6.7 and it compiles OK.
I think the issue might be to do with the fact that you're using Arduino.org's IDE, version 1.7.8.
The definition of GCLK_CLKCTRL_ID_TCC0_TCC1 is actually in an Atmel file called "gclk.h". It's referenced by the Arduino Zero's core, so you shouldn't have to add any includes to your sketch.
On my machine it's currently stored under the directory: C:\Users\Computer\AppData\Local\packages\arduino\tools\CMSIS\4.0.0-atmel\Device\ATMEL\samd21\include\component\gclk.h.
It might be that Arduino M0 Pro/M0 core doesn't reference this file? As I'm not using Arduino.org's IDE its difficult for me to find out where the problem lies. Have you selected the correct board type in the IDE?