Neither tactical option completely excludes the other, which is to say that your selection on coaching tactics determines the relative weight of the lineup chart and the AI selection. Therefore, since the weight difference between "starter" and "not entered into the lineup" is pretty significant, it was enough for the said behavior.
On the other hand, when you leave everyone off the lineup chart, they have equal weight, so the AI will rotate them entirely on his own weights.
It's certainly less than 100% intuitive, I imagine, but this behavior seems to be necessary so that the AI can sub correctly in games.
"I don't know half of you half as well as I should like; and I like less than half of you half as well as you deserve."