The Submit dialogue does indeed appear to only show (and presumably thus commit) changes in the Content folder, or at least, when I created a file in project root, it did not appear in the editor’s submit dialogue (though it did appear in git’s changes list).
My gitignore:
# Visual Studio 2015 user specific files
.vs/
# Compiled Object files
*.slo
*.lo
*.o
*.obj
# Precompiled Headers
*.gch
*.pch
# Compiled Dynamic libraries
*.so
*.dylib
*.dll
# Fortran module files
*.mod
# Compiled Static libraries
*.lai
*.la
*.a
*.lib
# Executables
*.exe
*.out
*.app
*.ipa
# These project files can be generated by the engine
*.xcodeproj
*.xcworkspace
*.sln
*.suo
*.opensdf
*.sdf
*.VC.db
*.VC.opendb
# Precompiled Assets
SourceArt/**/*.png
SourceArt/**/*.tga
# Binary Files
Binaries/*
Plugins/*/Binaries/*
# Builds
Build/*
# Whitelist PakBlacklist-<BuildConfiguration>.txt files
!Build/*/
Build/*/**
!Build/*/PakBlacklist*.txt
# Don't ignore icon files in Build
!Build/**/*.ico
# Built data for maps
*_BuiltData.uasset
# Configuration files generated by the Editor
Saved/*
# Compiled source files for the engine to use
Intermediate/*
Plugins/*/Intermediate/*
# Cache files for the editor to use
DerivedDataCache/*
# Don't ignore Plugin ThirdParty
!Plugins/**/ThirdParty/**
Still confused about the “View Changes” window, as it doesn’t show the actual changes (or if it does, it’s among the thousands of random engine files in the “Default Uncontrolled Changelist”).
Those files aren’t even on the same disk as the repository and project, much less under the same directory for git to track.