You can set the default charging amperage via the phone for a given location. Then after you drive to a different (assumed) Level 2 charging location you can set a different default charging amperage. The Tesla Model Y will remember the default charging amperage you set for multiple charging locations. This only applies to L1/L2 charging, not Supercharging. Sometimes the Tesla Model Y will lose the default charging amperage setting and revert to 48A. The specific Level 1/ Level2 charging station (could be the Tesla Mobile Connector or the Tesla Wall Connector) will automatically override this setting if it exceeds the maximum charging amperage allowed for the circuit rating. Even if the Tesla Model Y defaults back to 48A charging will not exceed 40A (in the case of your Gen2 Wall Connector.)
When two of more phones have the Tesla app installed, access to the same vehicle things can get sideways sometimes. Climate Control settings such as Scheduled Departure Preconditioning can be turned off from inside the Tesla vehicle, sometimes remain active because Scheduled Departure Preconditioning was once set on the phone. This may also be the case for the default charging amperage for a location. The Tesla Model Y enables you to set the Home, Work location in the Navigation System. If the Tesla Model Y is parked close to the Home location but not precisely where the GPS coordinates are set for the Home location then a different default charging amperage might have been saved for the second location.
You could try deleting the Home location from the Navigation system and see if the default charging amperage changes from 40A to some other value when using Scheduled Charging. If you still can't get this to work then Tesla may have to sync or delete the saved charging settings from their servers for your specific vehicle.