I think the answer is, it depends on what you are measuring.
I only have a couple data points, but none of our aircraft are identical. Things can easily be off 1/16? - 1/8?. If you want to ensure a flush, tight fit, I would wait. At the end of the build is not a time to start taking short cuts. You want the cosmetics to look as perfect as you can do them.
For the control cables, being off that same amount isn?t a big deal. If you don?t have your lower console, Geoff should be able to give you close measurements as to where the throttle will be located. Get some weed eater string and run it they way you want and measure it. Adding an inch for insurance shouldn?t be an issue.
There still will be FWF stuff to do once the controls are cabled up.
Out of curiosity, why does AFS have your lower console? I would have thought all they needed were the panel inserts.