Database
[{_id:1,otherField:true,settings:[{_id:11,values:[{likesFruit:true,likesMeat:true,}]},{_id:12,values:[{likesFruit:false}]}]}]
Query
db.collection.aggregate([{$addFields:{settingsAggregated:{$reduce:{input:"$settings",initialValue:{},in:{$mergeObjects:["$$value",{$reduce:{input:"$$this.values",initialValue:{},in:{$mergeObjects:["$$value","$$this"]}}}]}}}}},{$replaceRoot:{newRoot:{$mergeObjects:["$$ROOT","$settingsAggregated"]}}},{$project:{settings:0,settingsAggregated:0}}])