i enter a single entry to mongo, with Polygon which contains most of the earth:

db.test.insert(
{ loc : { 
    type : "Polygon" ,
    coordinates : [ [[-179, -90],[180, -90],[180, 90],[-179, 90],[-179, -90]]]
    }
})

then, when i query for a Point to get the Polygon(s) who contains it:

db.getCollection('test').find({
loc: {
$geoIntersects: {
$geometry: {
type: "Point" ,
coordinates: [0,0]
}}}})

i do not get any result. this is because mongo searches in the small part and not in the big one. if i query for a Point which is in the small section, i do get the result:

db.getCollection('test').find({
loc: {
$geoIntersects: {
$geometry: {
type: "Point" ,
coordinates: [-179.5,0]
}}}})

CRS can help me ONLY if i query for a Polygon. but in my case, I query for a Point.

I suggest to support CRS upon insertions of Polygons.