We have two examples of how First Enchanters interacted with the Knight Commanders assigned to their Circle in the games, that is not most First Enchanters.
The FE before Irving was able to plot with the Architect, bring the Architect into the Circle Tower, experiment with blight magic, and was obviously operating however he pleased. He was hoping to eventually take power by aiding Orlais in taking over Fereldan again.
Vivienne was a First Enchanter, and if that is how she views things, then she must have had little to no trouble with the KC assigned to her Circle.
Anyway, I do agree that Templars were overstepping their authority with some of the Circles, obviously, since the Circles are supposed to be run by the enchanters with the Templars just being a security force, keeping vigilance, and stepping in when necessary. That "necessary" part eventually being interpreted differently by different KCs... like Meredith...