I am not a database expert and have no formal computer science background, so bear with me. I want to know the kinds of real world negative things that can happen
The only reason atomic modifies work against a single-collection is because the mongodb developers recently exchanged a database lock with a collection wide write-lock. Deciding that the increased concurrency here was worth the trade-off. At it's core, mongodb is a memory-mapped file: they've delegated the buffer-pool management to the machine's vm subsystem. Because it's always in memory, they're able to get away with very course grained locks: you'll be performing in-memory only operations while holding it, which will be extremely fast. This differs significantly from a traditional database system which is sometimes forced to perform I/O while holding a pagelock or a rowlock.