Yes, but with #1 and #4 pistons rising and falling together then if you have the TDC mark on the flywheel lined up but the timing mark on the FIP is not in alignment and #4 is at TDC then rotate the engine 360 deg then magically #1 will be at TDC. I'd love to have the valve cover off to see to which cylinder compression stroke the FIP timing mark actually corresponds.
They could have timing of injection set at number 4. It is possible, as they can do whatever the manufacturer wants. As you said, if it was set at number 4 then the valves would be rocking on number 1.
I guess the point is to put the timing exactly as the manufacturer says at whatever cylinder they specify with both valves loose on that cylinder and the travelling companion cylinder at TDC also but with valves in overlap.
If the cylinder is in the correct location with the flywheel pinned, then the marks have to align at the gear train end or there is a problem Houston.
And all of this better be sorted out before the pump comes off cause if it wasn't, then its going to be a big timing job to do as you stated above.
Simon C