Regarding your question:

Also how can we Disable Default MongoDB ObjectID's Generation and _v?`

Setting versionKey to false in your schema will disable versioning.

const mySchema = new mongoose.Schema({
    someField: String
}, { versionKey: false });

All top-level documents require an _id. The _id serves as the primary key.

Note: autoIndexId: false only worked in older versions of MongoDB (before v3.4)