On a full size 'proper' cnc machine the limit switches will lock out the controller until someone with nouce can determine if it is safe to re-set them.
Remember you are playing with tiddly little stuff, but a full size machine can have several kilowatts of axis drive power that can shift things pretty fast and do very much damage.
On my Beaver Partsmaster the previous owner screwed up the Y limit switch setting, and it had managed to destroy a VERY expensive 40 mm ball screw and nut - if only those students hadn't fiddled ! (ex Bristol University)
On my Traub lathe the mass of the tool turret and slide mechanism is huge with servo drives of commensurate size - you don't mess with the limits on those unless you have very deep pockets

Good practise dictate that you have separate limit and home switches