system.indexes does not receive a UUID upon setFCV from 3.4 to 3.6 regardless of storage engine. Mongod 4.0 only exempts system.indexes from the UUID startup check if the storage engine is MMAP. This means that if a user creates system.indexes on mongod 3.4 or earlier when using wiredTiger, upgrades to mongod 3.6, then upgrades to mongod 4.0, mongod 4.0 will fail to startup.

One solution to avoid this issue is to drop system.indexes on startup if it fails the UUID check.