Try having an explosion (zero damage, zero visible effect) associated with the projectile, and have a Placed Object associated with the explosion. The placed object can be an activator with a script (perhaps with just an OnLoad event handler?) which notes its own X, Y and Z and handles these or records them for something else to handle.
A problem I ran into with my hoverchair mod is that some projectiles (bullets) worked fine, even when fired using the FireWeapon command. Others (rockets) would only detect and 'hit' objects if they were in the same cell as the player - when fired using FireWeapon, that is. For those I had to have an activator that looked like a rocket and moved itself with scripting, and a zero-damage bullet that 'painted' the location of the intended target using the method above, so the fake rocket could blow up when it reached sort-of-approximately the right position.
That little anecdote isn't directly relevent to Skyrim and Papyrus, but may serve to help you recognise weird game engine issues when they crop up, and to think of maybe-possible workarounds.
[edited for greater clarity]