G64 not read properly in RS247NGC_STARTUP_CODE

You can cover that with on_abort_command if you like.
linuxcnc.org/docs/stable/html/config/ini...sub:ini:sec:rs274ngc

Dear @radom! Thanks for that remark. If it is the case, then you are absolutely right that adding it in the startup code does not make sense. It could well be the reason why it seems not to work: it might be read in the startup code but then set back do default when enabling the machine.

But I don't understand the reason for this? The startup code is meant to bring the machine into a known and reproducible state, if the settings are overwritten by F2 then there is no point in it. Or is it only true for some commands?

The estop resetting G64 has been identified as a bug:
github.com/LinuxCNC/linuxcnc/pull/2742