marble sawmill

How do you want the two modes (saw/mill) to differ? They are both trivial kinematics but maybe you are thinking of disabling the C axis for the mill head?
Do you want to prevent the operator to move the Y axis with the saw down?

Unfortunately there isn't an easy way to prevent the operator from issuing commands to move the y axis when the z axis is down. The interpreter will accept commands to all axes defined in the ini file so you will need to handle that case in hal.
It should be relatively straight forward to prevent signals from reaching the motor driver whenever the z-axis is lowered below a certain height. However this will not prevent the internal position to change to the commanded value. If you do have positional feedback a following error will occur, if LinuxCNC is not aware of the physical position then nothing will prevent the program from continuing. If the z-axis is raised above the set value the y-axis driver is reconnected to the internal step generator but the y-axis will not match the internal position displayed in the DRO. The Y-axis would need to be rehomed unless you devise a more complex solution that will bring the internal position back to the value the y-axis was before it was disconnected.

Never mind the crunching/screeching sound, that is me, thinking...

The other option you could explore is using 'motion.feed-hold' or 'motion.feed-inhibit' pins.
linuxcnc.org/docs/html/man/man9/motion.9.html
This could, theoretically, stop any machine movement while still allowing the operator to jog the z-axis above the save height and resume normal operations without triggering a following error.
Given the dire consequences of having a saw go sideways you would want to thoroughly test whether this actually stops machine motion quickly enough. From a safety perspective it seems much better to disconnect the stepgen from the motor drive when the z-axis position is below the safe height rather that stopping the machine once the sideways movement has already started.


Of course you will want to inhibit jogging for the y-axis in hal regardless of how you stop the machine as that should be fairly easy to do.

Not as such but Joint and Axis limits can be changed using hal pins available in the ini. section after the gui has started. Note that the motion controller will only become aware of the changed values after a queuebuster command (eg M66 E0 L0).

[edit]
This is useful to clip or extend axis limits using M commands but it can not be used if the limits have to be updated continuously. For example if you wanted to change limits depending on the position of an other axis you would need to execute a queuebuster command through a hal pin connected to an MDI_COMMAND  which can only be done if the controller can switch to MDI mode at the time the change occurs. So you would again need to implement a safeguard in hal which will stop machine movements to avoid a crash but may require complex hal manipulation to recover from in an operator friendly fashion.

Thinking out loud here, tollchanges can be set to move joints/axis to a set position before making a change, can the same be done for Y axis when a move is requested to move Z axis up before moving?
Or using external offsets to move Z up before any Y move?