EDIT -- sorry, I didn't notice you are working on your front derailleur. The comments below were for a rear Di2 derailleur.

My first idea: Is there a spacer on your crankset axle? That would have moved the chainrings outward a little, limiting the adjustment range?

Instead:

(The Di2 "dealer" manuals are very good, and easy to follow for amateur mechanics. Download and save the pdf.)

Both the 6870 and 8050 manuals show the same front derailleur setup, turning a screw to adjust the cage position:

EDIT--sorry, this is one of the limit screw adjustments. Not a cage adjustment by itself.



then do the software micro adjustments if needed.
~~~

(for rear 6870 Di2)

My experiment didn't show any way to recenter the adjustment clicks.

In this Di2 adjustment thread, the original poster finally fixed it, by milling down the dropout to move the shifter a couple of mm inboard! See this post.
His symptoms were slow and noisy shifts to larger cogs, even with the adjustment range all the way to the inward side.

It appears that frames+dropouts can be made that won't adjust adequately with Di2!