Adjust oven rack to the centre position and preheat broiler. Line a broiler-safe baking sheet with aluminium foil.
Using a sharp knife, cut two shallow perpendicular cuts into the bottom of each tomato. Set the tomatoes on the baking sheet with the cut side facing up.
Arrange the garlic, jalapeños and shallots on the baking sheet with the tomatoes. Drizzle with one tablespoon of neutral oil and season with salt. Transfer to the oven and broil until the vegetables are significantly charred, about 15-20 minutes. Remove from the oven and set aside until cool enough to handle.
Remove the peels from the tomatoes and garlic. Scoop the seeds from the jalapeños and set aside for later. Add the peeled tomatoes to a large bowl and break up with a potato masher until fully pureed and few large pieces remain. Set aside.
Using a sharp knife, finely chop the jalapeño, shallots and garlic.
Set a small saucepan over medium-high heat. Add half a tablespoon of neutral oil and heat until shimmering. Pour over the pureed tomatoes and add the chopped jalapeños, shallots and garlic. Stir to combine and cook until slightly reduced and bubbly, about 5 minutes. Turn off the heat and transfer to a large bowl.
Allow the tomato mixture to come to room temperature before adding the chopped cilantro and lime juice. Taste to adjust for seasoning, adding salt and pepper where needed. If you would like to increase the heat in the salsa, chop and add the reserved jalapeño seeds in increments, tasting with each addition to ensure you reach the desired level of heat.
Transfer the salsa to an airtight container and refrigerate for at least 30 minutes before serving.