All the probe, or your tool height plate do is send a signal to the computer - so you can set them up anywhere you like. The thing that makes the difference is what happens next.
If you are using the same program to measure your tool height as you are for your probe then there could be a clash if both use the same input. If the probe is just a switch, and the tool height fixture is just a switch, then there will be no problem - since both are open then one closes when it touches, then there is no feedback to the other.
If there are some electronics in the probe or the tool height fixture, there might be some feedback and in that case,I, personally, would use a Nand or an Or CMOS chip to combine the two signals - the cost is a few pence. The chips have numerous inputs, but only one output, and all you do is lead the inputs to the chip, and the output to the breakout board. The chip isolates the inputs, but as it's name implies if one input OR the other signals then it passes the signal to the computer. (The Namd chip is the same, but inverts the signal)
If you are using a seperate program for your two sensors, then use seperate pins as inputs and configure accordingly.