The issue is really with iTTL balanced fill flash versus Standard iTTL flash. In iTTL balanced mode the flash will use preflashes and rely on distance information for accurate exposure. With non-CPU lenses distance information is not available. For iTTL balanced operation the metering mode must be either Matrix or Center Weighted. Spot metering is not available and the flash mode will automatically switch to Standard iTTL mode. In this mode distance information is not used and the flash intensity is reflected from the main subject. This is why flash exposure is more accurate when spot metering changes the flash to Standard iTTL.
I tested this operation this morning by putting an AI 85mm f1.8 lens on my D300 and using the SB800. The lens info was entered into the non-CPU lens data menu.
First, when changing the metering mode from Matrix or Center to spot, the flash automatically changed the flash mode from balanced to standard.
Second, I took a series of photos starting at 10 feet to 15 feet to 20 feet from the subject. In matrix mode the photo got a little darker as I moved away. In Spot metering mode the exposure stayed exactly the same as I moved away.
For my general shooting I use either Matrix or Center weighed metering. Sometimes when I take a flash photo, I forget, and it turns out too dark so I have to put it in Spot metering.
Over half of all my photos are taken with manual focus lenses. When using flash I must use Spot metering. I never paid attention before but it's because the flash is switching to Standard iTTL mode. This has worked for my D200, D300, D700, D2X and D3X. I only use the SB-800. I need to look into the D800 and flash further however the manual has the same Flash Control Mode language as in all the other camera manuals.