Translation:I like the flag and I also like the blue color.
You have a good point. I am a native English speaker and "the color blue" definitely sounds more natural.
However, if "la bluan koloron" refers to the coloration of the flag, rather than the general concept of the color blue, the phrase is better translated as "the blue color" or "the blue coloring."
I believe the sentence is saying "I like the flag (design, or aesthetically) and I also like the blue color (of the flag)" So, yes there would be a legitimate difference in meaning. If you said that you "also like the color blue" that comes across as more of an unrelated fact than it does a fact related to the color of the flag.
I agree the color blue is more natural in the general concept. To be more clear and natural in English about that shade of blue a person might say: I also like that shade of blue. or I also like that color of blue.
Please note I am not saying you should use these in the translation, just that they are more precise and clear in English, I do not know enough Esperanto yet to say that using "that/ke" is more clear than then "the/la".