Photos and Image Capture app allows you to change the settings for a particular device and when you format your card, it is recognized as a new device and hence, the Photos app is back to default settings.
This is how these applications have been designed by Apple.
Settings in Lightroom are fine but the Apple default applications overwrite Lightroom settings and pop-up Photos App instead of Lightroom.
I am not sure if there is a way to disable Photos App for all devices.
You need to get in touch with Apple for this.
I have already fed back the situation to Apple on one of their forms.
Do you know of any other way to do so where you can actually speak to someone about it?
May be you can call Apple support for this and confirm from them if there is a way to disable Photos App for all devices.