Combine water, vinegar, sugar, red pepper flakes, and garlic in a small saucepan over medium heat; cook and stir until sugar is dissolved and sauce is slightly reduced, about 5 minutes.
Heat a skillet over low heat.
Spread butter onto 1 side of each bread slice. Spread cream cheese on the opposite side of 1 of the bread slices. Layer Cheddar cheese and pickles on top of the cream cheese layer. Drizzle 1 to 2 tablespoons sauce on the other slice of bread on the side opposite the butter; place bread on top of pickle layer, butter-side on the outside, creating a sandwich.
Cook sandwich in the hot skillet until cheese is melted and bread is browned, about 5 minutes per side. Remove top bread piece, add tomatoes to middle, and close sandwich.
