I'm having issues with large file uploads in SharePoint 2016. We've increased the limit to 2GB and set the executionTime=999999.
We've noticed that the "file uploading, won't take long" dialog box stays up for a really long time, so we close it manually and the file is there but checked out.
We've noticed that this is only an issue using the External URL, not with the Internal URL. The External URL goes through a WAF first so we're thinking maybe that's the problem but we haven't tracked it down yet.