It shouldn't matter, it will remove 4.6 and install the new agent. From memory I had issues with 5.0 and 5.0.2 (188.8.131.523 I have found to be ok thus far but am early on with deployment). 184.108.40.2066 is what we run mostly but you will need 5.0.2 minimum from memory if you run Win 10.
What will really matter is EPO, VSE and other endpoint products and what agent, epo, vse etc are compatible.
You can see the compatibility matrix linked below:
Upgrade path is better via 4.8.0 to 5.x, both version can co-exist on the same epo