Can we shift talk to solutions in enabling UNO shields to be compatible with a mega's slightly altered pin layout?
Sure. It involves pin bending. On the shield that does SoftwareSerial on pins 2 and 3, bend those pins so they don't fit into the slots. Solder a wire on each to connect them to the TXn and RXn pins, and use Serialn to read them.
Do the same for other conflicting pins.