Your average user isn’t likely to venture into this file to make any modifications, so it would be safe to assume that anyone who applied those settings knew what they were doing.

You're kidding right? The WordPress world is full of people who do a quick google search, arbitrarily apply config changes and who knows what else and then bring their whole site crashing down around them. I think WP Engine are spot on to disallow this forthcoming feature.

I don't use WP Engine myself, I much prefer the freedom of managing my own sites, but for your typical WP Engine customer, restricting them this way is the right thing to do.