Isn't it strange that in ME1, Shepard is allowed to be a Spectre while still being in the Alliance military?

It's been a while since I've played the games, so maybe the series does address this at one point and I just don't remember, but I just started thinking about this and it seems strange to me. I think the Council probably expects that the average Spectre operative to be somewhat biased towards their own species, but Spectres are supposed to act for the good of the galaxy regardless of biases. Shouldn't this be considered a conflict of interest? Also, that Alliance admiral guy who inspects the Normandy treats Shepard like a subordinate, even though as a Spectre, Shepard outranks them? Seems slightly confusing.