Du skal definere arrayFilter for hvert niveau af indlejring, prøv:
db.Test123.update(
{ "someKey" : "someValue" },
{ "$set": { "someArray.$[someArrayDoc].someNestedArray.$[someNestedArrayDoc].level": "Senior Developer" } },
{ arrayFilters: [ {"someArrayDoc.Company": "Company1"}, { "someNestedArrayDoc.name": "Nandhi" } ] }
)