Peel the tomatoes: Bring a large pot of water to a boil over high heat. Meanwhile, fill a separate bowl with cold water and several ice cubes. Score the bottom of each tomato with an X. Once water is boiling, drop tomatoes in for 15-30 seconds; remove with tongs and immediately plunge into ice water. Slip off the peels with your hands, then roughly chop the peeled tomatoes.
Add the tomatoes, apple, chile flakes, garlic, ginger, sugar and balsamic vinegar to a medium saucepan set over medium heat and stir to combine. Bring mixture to a boil very slowly, then lower heat and gently cook, uncovered, for about 40 minutes, stirring occasionally to prevent scorching, until the mixture is thick and jammy.
Meanwhile, submerge three 1-cup canning jars, along with their lids and ring bands, in a large pot of boiling water and sterilize over high heat for 10 minutes. Transfer sterilized jars, lids, and bands to a clean dishtowel.
When the jam is ready, remove from heat and, if desired, use a potato masher or fork to break down tomato and apple chunks to your preferred consistency. Fill each jar with hot jam, seal and leave to cool. Stored in a dark, cool place, jam will keep indefinitely; once opened, a jar will keep for about a week in the fridge.