In previous iOS 10 beta's you would still get the message but the download would continue as normal. I have to confess, I haven't done a 100+MB app update over cellular since beta 4, has the message now gone as well?
* update: just updated a 186MB app over cellular, worked fine without even a warning or message. But tried to install a new app, CSR racing 2, and got the message about being over 100MB and it didn't download.