I completely disagree. With the things you said right there, there would be a huge difference. An alternate commander of the west would perhaps use his authority more often than Johnston did and change a great many things.
Bragg and Pemberton acted independently of the Department Commander's authority, and Davis failed to re-establish the Department Commander's authority over them because he still permitted them to bypass that office entirely and send their reports and request straight to Richmond.
Anybody who becomes Department Commander will have to deal with the same problem where their authority to act has not been fully recognized and Davis will be able to overrule them on any matter - as an example, neither Bragg or Johnston wanted to send Carter Stevenson's big division to Mississippi on the eve of Murfreesboro but Davis did so inspite of their opposition, and Johnston had wanted to reorganize the department into two smaller department but was prevented from doing so by Davis who didn't think it was a good idea.
That Johnston did little more than quartermasterly work during his time as Department Commander was as much a reflection of Davis's reluctance to give away any real power as it was a reflection of Johnston's own sensibilities.
Also, the Department Commander's job was reactivated as a consequence of Johnston declaring himself fit for service and if he's dead there's no reason to believe Davis simply wouldn't keep it defunct and handle thing himself as he had been doing previously, which means there would be even less reason to expect any major differences in 1863.