If I deposit cash with an ATM which reads the bills one at a time, however, is the transaction more likely to later get changed?
Ultimately, for a variety of reasons, the answer to this is no. There is not a statistically significant difference in counterfeit detection between ATM deposits and over the counter deposits at branches. I'm saying this based on having access to a large set of benchmarking data from US-based financial institutions, including data on fraud detection.
In other words, if your concern is purely about getting caught when depositing counterfeit money, there is no difference between your chances of getting caught when depositing at a branch versus via an ATM.
In fact, to take that one step further, if your ultimate concern is "I don't want to get caught trying to deposit counterfeit currency" then your best focus is on making sure you never receive counterfeit currency in the first place. In other words, don't worry about your chances of getting caught when trying to deposit the bills - instead, focus on screening any currency that's handed to you when you receive bills.
And, on that note, to continue the reference to actual hard data, more counterfeit bills are caught at origin (i.e. the person first trying to insert them into circulation is caught) than from others handling the bills down the line (i.e. an innocent third party getting caught trying to deposit a counterfeit $20 that they didn't know was counterfeit). The notable exception is counterfeiters who target person to person transactions as a way to circulate the bills (i.e. they pay you $100 in fake twenties to purchase a TV you listed on Craigslist). The easiest way to protect yourself from that is to conduct all person to person transactions with unknown parties right at a bank, so you can immediately, in the presence of the buyer, deposit the cash. If a buyer won't agree to that, well then - you need to find a new buyer.
Counterfeit currency is a tiny fraction of fraud, so if your larger concern is getting caught in fraud, it's probably not the best place to focus.