Tienes que $unwind para aplanar los _ids extranjeros tanto escalares como del subdocumento y agregar $group etapa al final de la tubería para recuperar la estructura original.
$first acumulador para mantener los campos y $push con $arrayElemAt para acumular los valores de la matriz para ajustar $unwind
var linkedModels = [
{
"$match": { "del": false }
},
{
"$lookup": {
from: "charnpcalign",
localField: "align",
foreignField: "_id",
as: "linked_align"
}
},
{
"$unwind":"$classes"
},
{
"$lookup": {
from: "charnpcclass",
localField: "classes",
foreignField: "_id",
as: "linked_classes"
}
},
{
"$group": {
"_id": "$_id",
"name": {"$first":"$name"},
"align": {"$first":"$align"},
"classes":{"$push":"$classes"},
"carrying":{"$first":"$carrying"},
"linked_align":{"$first":"$linked_align"},
"linked_classes":{"$push":{"$arrayElemAt":["$linked_classes",0]}}
}
},
{
"$unwind":"$carrying"
},
{
"$lookup": {
from: "item",
localField: "carrying.itemId",
foreignField: "_id",
as: "linked_carrying"
}
},
{
"$group": {
"_id": "$_id",
"name": {"$first":"$name"},
"align": {"$first":"$align"},
"classes":{"$first":"$classes"},
"linked_align":{"$first":"$linked_align"},
"carrying":{"$push":"$carrying"},
"linked_carrying":{"$push":{"$arrayElemAt":["$linked_carrying",0]}}
}
}
]
No necesitas el $unwind en la matriz escalar (classes ) en la versión 3.4 y puede reemplazar {"classes":{"$push":"$classes"}} &{"linked_classes":{"$push":{$arrayElemAt:["$linked_classes",0]}}} con {"classes":{"$first":"$classes"}} &{"linked_classes":{"$first":"$linked_classes"}} respectivamente.
