You can easily ensure the behaviour you desire by using TrimEnd:
var baseDir = AppDomain.CurrentDomain.BaseDirectory
.TrimEnd(Path.DirectorySeparatorChar) + Path.DirectorySeparatorChar;
To be optimally efficient (by avoiding extra allocations), check that the string doesn’t end with a \ before making changes, since you won’t always need to:
const string sepChar = Path.DirectorySeparatorChar.ToString();
const string altChar = Path.AltDirectorySeparatorChar.ToString();
var baseDir = AppDomain.CurrentDomain.BaseDirectory;
if (!baseDir.EndsWith(sepChar) && !baseDir.EndsWith(altChar))
{
baseDir += sepChar;
}