There are further arrays (like array of cObjects for subparts and marks in templates)
They all define another level of elements in your typoscript. The kind of array may give you a hint what index and what kind of values are expected.
Sometimes the index is ordered for evaluation (e.g. COA, layoutRootPaths), sometimes it does not matter (e.g. marks, subparts) or are evaluated in the order of the typoscript (e.g. includeJS). As you could have multiple kinds of array in PHP each can be evaluated in multiple ways.
The kind of values (in the documentation) depend on the further evaluation. Simple integer, strings, cObjects, ...
Not everywhere you are able to add stdWrap functions (so values evaluated in the core should have it).
As you already mentioned: typoscript is scanned and stored as multidimensional array.
Each part of (core-)code evaluates this array with an individual logic. So the interpretation of an array is done individually.
And until now there is no full consens about which kind of arrays are representative or typical to be an own type. An unification would probably need code changes, in core and in multiple extensions.
For optimization of the manuals you should open a forge ticket requesting an explanation in the manuals with the kind of arrays you found.