the input impedance on the MC low setting is 2.5 ohms.
No it is not.
When Luxman says the MC Low is 2.5 ohms they are referring to the cartridge's internal impedance, not the load the cartridge sees. The internal impedance of the Apheta is 10 ohms.
It seems like the 40 ohm indicated for the high setting would be a closer match to Rega Alpheta 3 recommended settings?
Not necessarily.
The Luxman MC inputs are designed for low impedance ( 2.5 ohms ) and high impedance ( 40 ohms ) cartridges.
Examples of low impedance cartridges are Koetsu's 3-5 ohms, Mysonic Lab 2-3 ohms.
Examples of high impedance cartridges are Denon 103 ( 40 ohms ).
Since the Rega APHETA 3 is 10 ohms, the low MC setting is probably closer to ideal. The Rega needs to see 100 ohms - try measuring the input impedance on the phono to see what the load really is on the "2.5 ohm" setting.
In reality as mentioned above, getting the gain right is as important as load, so nothing wring with trying the different settings and using your ears to decide the optimum settings.