(I am cutting a ton of very informative stuff from you out of this reply because this one particular bit really goes to the crux of the matter)
If Jimmy Decker want to send a message while impersonating Johann Corp then Jimmy Decker can mark Johann Corp and successfully use Spoof Command.
Can he? Spoof Command (SR5, p.242): "You spoof a device's owner's identity, making the device think that your command is a legitimate one from its owner. <stuff about marks, etc, snipped> This trick only works on devices and agents, not IC, sprites, hosts, personas, or any other icons." Can Jimmy Decker use Spoof Command in this instance? If he *can*, then why can't he get the requisite marks on the commlink directly and use Control Device to send a message?
If he can't while Johann Corp has his persona loaded, then what about when Johann moves his persona to another commlink (perhaps he thinks that he left his Sekretär in his summer home in Prague and didn't bother trying to actually locate his despite being the owner and finding the physical location of his property is a trivial matter), leaving Alistair the Agent running? Assuming that Jimmy has the requisite mark on Johann (and assuming that Johann is actually the owner), he can certainly use Spoof Command on Alistair in order to have Alistair send a message on behalf of Johann, but Jimmy wants to skip the middle man and send it himself. Can he use Spoof Command on the commlink? (Yes, I realize that the agent acts with the authority of the owner while loaded and could most be Spoofed to have the commlink send a message *as* Johann).
If not (because the commlink is under the umbrella of Alistair the Agent's persona), then does this mean that someone who loads an agent onto their rig-equipped vehicle need to unload the agent before they can jump into it? What about when they want to let their rigger buddy (who they've Invited three marks from on said vehicle) jump in?
Yes, some of these examples are extremely corner-case or obtuse, but I'm legitimately trying to get to the bottom of this because my group has been (apparently) playing wrong since SR5 came out (and the way that my group has been playing has seemed extremely logical to us).