Even though he may be alive in Marvel TV show that he helped create. Yes, he also acknowledges that it's confusing.

He basically said that writing Coulson into an already packed film would have been too difficult and required him to write a whole B-story where they discovered his status that he was alive. He couldn't just show up at the end with the cavalry, with no explanation.

But yes, they could have at least included Fitz in those scenes from the Helicarrier.