It'll be a little off, but if you always do it that way and reference to the same pot values, you'll have at least a self consistent database.
I do not use installed values for my database, but I will regularly do spot checks (for instance just to make sure everything is working before I screw the pickguard back on and tighten up the strings! ARRRRRGH!!!)
Make sure all of the pots are on "10". Also, what I've done is clip off an old guitar cable, so I have an RCA plug on one end and bare wires on the other. Just plug this test cord into the guitar jack and test the DCR (or more preferably ACR and inductance!) across the exposed leads.
If you don't want to make a test cable, just plug in a normal cable and measure the DCR across the tip (hot) and the shaft (ground) or really any grounded part of the guitar.
Depending on where the switch is wired in the circuit, you can sometimes measure them while in the guitar by making sure the pickup you are measuring is in the "off" position at the switch.
For this to be so, the pickup has to be directly wired to the switch before anything else, you simply put the switch so that the pickup you are measuring is in the off position, then measure between the hot wire of the pickup at the switch and ground.