Z probe height in EEProm vs Z offset in Slic3r

EGropp

I had to rebuild the bed on my printer and have been trying to get the z-probe height back in order.
I went through the tutorials that i found to get the correct numbers but, when i put them into the firmware and home the z axis, the nozzle homes, then travels lower than the bed height, crashing the nozzle into the bed.
If i set the z probe height to 0 and add the measurement to the z offset in Slic3r, i actually get pretty good first layer adhesion.
The question is, why would the numbers be different in the firmware settings that in SLic3r?
The configuration i ended up with.. I moved the z probe sensor closer to the bed, so at machine home (z0) the nozzle is actually above the bed. After all of my measurements, the nozzle is actually 2.8 mm above the bed.
Why would the 2.8 nozzle height be different than a 2.8 z offset??

Repetier

Did you set this in eeprom.

Also make sure to configure home to go first up before homing so you trigger from low to high and not start with high, also seconds homing should normally fix that as well (also > z probe height to be on safe side). Otherwise it might end up lower then 2.8 just because you started triggered. Make also sure bed coating is 0- But homing with z probe has many tiny kicks you need to configure right or parts are not executed or defined wrong. It is much easier to have z max endstop + z probe.

EGropp

Yep, I set the z probe height in EEPRom, moved z up 10 then re-homed. i was able to adjust the measurements to make the nozzle not crash through the bed, but that process was a hit / miss deal and seemed less than accurate.
The bed coating is 0 (i've never changed that one at all).
Would it be better to home z to the top? (i have heard that it was but some complained about the time it took). When I tried to reach out to the printer manufacturer, they said don't do it, this now seems to be more of a personal preference of the manufacturer than anything.
I think the biggest question I have hear is "What would be the best option?" I have extra switches so i can add one to the top of the gantry, i just dont know how to get that done in the firmware yet (Not in front of the printer at the moment).

Repetier

Vendors don't like users modifying printers, so the answer is no surprise. The longe rhoming time at startup is the only disadvantage of z max homing. Advantage is that you can at least thoretically continue aborted prints as you can now home even with a print still on bed. You would of course still need to know where to continue and remove the start of already printed part to continue.

If you have a firmware config for ou config tool, changing this is quite easy if you know how to add a hardware endstop. Just unset z min endstop and add z max endstop and set homing direction to 1. z probe still uses same pin. Works of cours eonly if board has support for max and min pins, not all have enough pins.

You should also test repeatability. Go to center at 10mm height and repeatedly rung G30 and see in log how much results vary.