Clean is the base theme that Essential inherits from, so they share a lot, but Clean is more bare-bones, like the Base theme that many other themes inherit from.
Regarding your questions, the first "supportscssoptimisation" is related to an extra step of CSS minification. Moodle sometimes has CSS for the same things in two places, e.g. the size of an element might be set in the Base theme, then the color of the element set in the Standard theme and then all that CSS will be combined into one file. Moodle has a process that will search through your CSS and combine:
.example { width: 60%; }
... lots of other CSS ...
.example { color: red;}
into
.example { width: 60%; color: red;}
But this process had some issues with more advanced CSS (I think media queries confused it? Or pre-minified CSS?) so themes can opt-out of this step if it causes problems.
The second, "yuicssmodules" lets you opt out of including the YUI CSS if your theme doesn't need it. There's not much to the YUI CSS, most will be duplicated by any standard CSS framework you import. It also lets you avoid some bugs created by this CSS (e.g. MDL-27774, which is fixed in Clean and it's child themes, but not in Base/Standard etc.)
You can find these documented in the theme_config class here:
https://github.com/moodle/moodle/blob/master/lib/outputlib.php#L115
There used to be online docs for this (just the same info but presented better), but they seem out of date now and don't have the newer additions:
http://phpdocs.moodle.org/HEAD/core/lib/theme_config.html