Where different / how should I store a fresh tomato in my 'fridge?

No problems with storing them together. I store mine in the salad crisper drawer but I remove all wrappings and place in separate trays in the drawer. It's not for cross contamination but one can make the other ripen quicker which you don't want if you want to keep them longer. I also place a piece of kitchen paper in the bottom of each container to stop condensation but if your fridge has a humidifying thingy then you don't need to.