Flywheel timing mark wrong on HUP

[Malcolm Towrie]

I just worked on a HUP. It ran ok, but I decided to check ignition timing. I got #1 on compression stroke and then rotated the flywheel until the ball bearing insert in the flywheel lined up with the indicator pointer. Then I rotated distributor to match the rotor to the wire to #1 plug. It wouldn’t start. Nothing, except the starter would occasionally stall on the compression stroke, indicating timing was way too far advanced.

So I went back to basics and found TDC on #1 firing with a leak-down gauge, which is pretty accurate. I marked the flywheel with the real #1 TDC with yellow paint, and set up the dizzy for that. It then started and ran fine.
The true #1 TDC firing was about 90 crank degrees off from the ball bearing mark.
Just wondering why the flywheel was so far off? According to the manual, the flywheel locates on 3 dowels and 6 bolts. There’s no mention of indexing the flywheel to the crank to ensure the TDC mark is correct.
Are the dowels offset to ensure correct indexing? Or the bolts? I guess not.
Did the flywheel on later engines fit, but with different indexing?
Malcolm