The limits switches can be fairly close to the mechanical limits as long as you ALWAYS have soft limits turned on and reference the machine before use.
The deceleration time for the steppers is in you motor tuning.
Steppers don't coast, but need to decelerated in a controlled manner, which Mach3 does once set up correctly.
During normal operation, after referencing the machine, you never will hit the limits, if soft limits are enable.
Hitting limits instantly stops the stepper motor and if running above a critical speed will overshoot steps during the abrupt stop that occurs.
As for the .100, the value used depends on how well the machine is setup, and the performance of the steppers.
I think .100 is very small, and many stepper/controller combinations, at speed can require much more than .100
A rubber donut on the leadscrew can make a compact bumper, at the expense of losing a little travel.
If using high powered motors this is good insurance against damage.
I have seen older machines with a coil spring that gives a controlled energy absorption during a limit stop crash.
The spring idea I have seen on Pratt and Whitney stepper driven mills - circa 1970's
My powerful machine will use donuts. 6000mm/min with 25mm screws can do damage.
Super X3. 3600rpm. Sheridan 6"x24" Lathe + more. Three ways to fix things: The right way, the other way, and maybe your way, which is possibly a faster wrong way.