For the last time:

Colin Kaepernick did not lose his starting job to Blaine Gabbert. Kaepernick was injured. Kaepernick was put back into the lineup in Week 6, after he recovered from offseason thumb, knee and shoulder surgeries.

Kaepernick lost significant amounts of weight and muscle mass due to the surgeries, and needed time to bulk back up. He did compete for the job in training camp, but it was clear he was not healthy enough to handle the full-time load.

Now, it IS feasible that Gabbert could have stolen the starting job away from Kaepernick had he played well for those first five weeks -- it wasn't a "legend waiting to get healthy" situation. But he didn't, and when Kaepernick was good to go, he was the starter.

Chip Kelly back then (late September):

"I don’t think he’s ready to go full-time. He’s continuing to work on it... His playing weight has been around 225, and he’s not at that right now. He had a serious layoff in terms of being able to medical rehab." https://www.espn.com/blog/nflnation/post/_/id/215799/chip-kelly-colin-kaepernick-not-100-percent-right-now