If you have the correct cast alloy sump on your 4.6 I would be using the 3.9 dip stick as it is shorter - assuming the dipstick is from a 3.9 with the tin sump.
Here is a pic of the two dip sticks side by side with the tops (out of frame) aligned - the longer one is the 4.6 and the shorter one is the 3.9. As mentioned this assumes the 4.6 has the correct alloy sump and correct length dipstick tube and the 3.9 has the correct tin sump and correct length dipstick tube - these are from a Disco 1 and Disco 2 - obviously engines from different makes such as TVRs etc or engines that have had parts mixed then that confuses matters.
The length of the tube on my 3.9 is 11.5" and the 4.6 is about 13" (hard to measure with the engine in the vehicle) so if using a standard sump with standard tube you are probably over filling your sump but there are many variables. if you have a standard alloy sump and the correct tube just get the correct dip stick from a wrecker.
Capacity from dry is 6.6 litres but refill is 5.8 litres.
Garry