Change default set-up home from 0,0,1 to 0,0,0.25

The safest home position is with Z all the way up.

If the 0.25 is just for a tool change, think hard about all possible machine movement scenarios.
E.g clamps, workholding, tall work piece.

You don't want some g code to tell the machine to go to home (e.g. G53 X0Y0Z0) and smash into clamps etc.

The most common way to setup a machine is for Z0 to be at the top of the Z travel, and for all Z travel to be negative.

If you are not already familiar with the difference between
G53 / machine coordinates
G54-G59 / work coordinates
Then I suggest you read about them as it's very important to understand

hi Pippin, I do tiny stuff on a Sherline 2000 with very small bits. I've found the best way to set the height is to roll a piece of .250 drill rod back and forth under the bit until the bit just clears. If I set Z to .250, All I need to do is start linuxcnc, home all axes and then turn everything on. It may seem clunky, but this is not a production environment and I can take the time needed to not destroy bits and gouge workpieces.

I picked up this method routing PCB;s where the depth of cut is critical.

you can still home at top of travel but use g54 offsets and touch off the Z axis to 0.0 at the height you want.