The plugin vim surround allows you to choose whether you want spaces and parenthesis or just parenthesis. You can disable it by using other mappings; actually you pasted them in your question, as the second and third examples.
This is actually a pattern in the mappings of this plugin: if you use the opening character - e.g.:
[ - them it will include spaces. If you use the closing character - e.g.:
] - them it won't include spaces. The aliases for these blocks (
r) also doesn't includes the spaces, probably because most of time the people (like you) doesn't want the spaces.