it's quicker to throw down improvisation than to cripple yourself and write it one note at a time or w/e
And to be honest, the master has to use a bit of both (improv and thought) in order to achieve what the situation calls for.
quite honestly, i make some of my best music (personally) when ever i just let things happen. if something is completely off, i'll have to go in and change some things theory wise. but i try to aim for getting things write when ever i play them, so i don't have to always go back over and do it. it's music after all.
and quite honestly, if you're questioning where or not it's counterproductive to think, i don't think that's really a question you should be asking. because at any level, you're always thinking. weather or not it surfaces into your inner dialogue is actually what's happening.
understanding every thing, is the enemy of progress.
No one is asking that of you, but yourself. so then yourself is getting in the way of realistic goals.
take a step back and consider what you're capable of, and then move from there. your capacity to be more skillful will grow over time with the right counsel, until you'd of exhausted their teachings.
If you don't know the why, you cannot do it well.
therefore, balance is what you should consider to achieve a more optimal understanding of your music that you create.