Phantom B44 overhang concern

When I align my Ortofon A90 in the Phantom with the mint - or the Graham protractor - it ends up in a very similar position to your Shelter. Same with the Ortofon Jubilee.
The Denon 103R on the other hand is positioned mid-way in the headshell slots. I'd say the Denon conforms to the standard 'mount to stylus tip' distance - the Ortofon and Shelter do not.
Of course this is why slotted headshell mounting is provided by tonearm manufacturers (except SME who ignore this) - so you can maintain the correct 'pivot to stylus' distance with cartridges of varying 'mount to stylus tip' measurements.

You seem to be suggesting that all cartridges, for all alignment geometries, should have their screws in the centre of the fixing slots?
If that were so, why have the slots?
You'll find different cartridges and different geometries will be accommodated by the screws 'moving' within the slotted holes.
Please don't lose a moment's sleep over this.

Also, depending on your turntable, the spindle to pivot distance of the arm, may not be 100% accurately set thus resulting in some adjustment required in the overhang geometry?

Don't worry. The Alignment is based on the position of the needle. When you want a cartridge which is more "in the middle" of the slots, try a Lyra Helikon :-)