The use of the indefinite article as in the examples you list is possible with many uncountable nouns, and so is not peculiar to command. This is the best reference I can find at the moment, although the subject is somewhat addressed here and here.
Essentially, when an uncountable noun is limited in some way, it becomes a countable subset of the concept the noun represents:
a healthy respect,
a doomed love,
a heavy fog,
a dark coffee,
an unquenchable thirst. This is what is happening in all your examples (except perhaps the last). Although
command of English may be uncountable generally,
a very basic command or
a brilliant command are countable (or at least can be) because they exist in comparison to other (modified) commands.
In my opinion, uncountable nouns are a very fuzzy concept and the borders between uncountable, countable, and mass nouns are not clear cut. For instance, compare
We saw fog outside.
Outside, a fog rolled in.
In the first sentence, fog is an abstraction (or at least a general concept); in the second, the specific fog in the location is being referred to. And in both sentences, the use of the article could be reversed without really changing the underlying meaning. What would change would be a slight nuance that may, or may not, be important, given the context. In the second sentence, using the article makes the fog in question slightly more concrete (so to speak): maybe the fog was expected, or maybe (if this were part of a narrative) the presence of this fog at this time is important to the story.
I point this out because of your last example, which does not use the article, but, in my opinion, would be correct either way. As written, good modifies the abstract concept of command, but if the article were used, the command referred to would no longer be abstract, but a subset, or a particularized type of command. There would be the (subtle) implication that this good command is being compared to either a worse command or a better command.