Roast jalapeno over a gas flame or under broiler until blackened, turning as needed. Transfer to small bowl, cover tightly with plastic, and let steam until cool enough to handle, about 10 minutes. Peel, seed, and stem pepper. Reserve any liquid collected in bowl. Cut pepper into 1/8-inch strips. Set aside.
Peel mangoes; cut into 1 1/2-inch pieces. Transfer to medium saucepan. Add onion, raisins, vinegar, and sugar; stir. Place over medium-low heat; cook, stirring often, until sugar has dissolved and liquid has been released from mangoes, 8 to 10 minutes.
Seed and devein fresh hot peppers. Cut into 1/4- to 1/2-inch pieces. Add to mango mixture. Add reserved pepper strips and any reserved liquid. Stir into mixture with lemon juice and zest, ginger, cinnamon, salt, and pepper. Reduce heat to low, continue cooking, stirring to avoid scorching, until mixture has thickened, 35 to 50 minutes. Remove; transfer to medium bowl. Stir in almonds. Let cool to room temperature. Transfer to an airtight container.
Chutney will keep, refrigerated, for 4 to 6 weeks.