Ah yes
Ah yes, so it does. It had already become so automatic for me I had 'forgotten that that initial dialogue prompt is called "Command."
I also agree that companions (Dogmeat anyway) has a somewhat annoying habit of running right in front of "me" (my cursor actually) a lot of times that I'm just about to interact with a corpse, thus causing me to open up the "command/dialogue" menu for Dogmeat, instead of the container interaction. Having not played on console, and also having not done the most recent patch, I am not sure how translatable this is to other platforms or to the revised keybinds in the patch.
But here is how I cope:
1. Avoid pointing at Dogmeat in general
2. When I point at him, almost always immediately click "E" (the default key I think). If he is far away, this opens seemingly only one thing "Go here" (which doubles as "Stay" if you do not point the cursor somewhere else and click "E" again rapidly after the first time). I use this to my advantage as putting the cursor on him generally isn't difficult (as long as he is in sight) and telling him to stay (else to "come here") is generally a suitable interim solution to whatever I want him to do, which is usually either stop doing something that will blow our cover, else to not activate mines or to allow me to trade between inventories.
3. Luckily this also works in reverse. If he has been told to Stay (and he generally does stay, though not always) then pointing at him and typing "E" then quickly typing "E" again will tell him to come. I then have to type "I" (other keys might work I don't know) which is my key I have binded for Inventory in order to escape out of command/dialogue menu.
So if he is sitting at stay, I just point at him, and Type: "E," "E," then "I" in quick succession and I can get him to follow along again, even while I'm just running toward/past him in autojog mode.
Given all the platforms and different input devices the game has to work with, I don't know for sure how this system could be improved on. It seems like making EVERYTHING that has a keybind rebindable might be a good thing, but I'm not sure if that is problematic somehow. When people first started commenting on the UI, I saw a lot of comments (before I had the game) that "OMG Betheda!? Why did you make all the keys hard binded!? Let us rebind all the keys!"
I'm a bit puzzled by those comments now, and I think they might in part have reflected incomplete understanding of the UI (which I suffer from no less than anyone else I'm sure). But in my experience, -most- of the keys ARE rebindable. The fact that "E" stays a default "activate button (for example when scraping stuff on the ground) but that it doesn't say so in the Help was a source of mild annoyance for quite a while (as I was doing left-hand gymnastics with my keyboard in order to type "R" to scrap then "Enter" to complete the action, while using my mouse in right hand to point the cursor). Some kind soul pointed out that I could "E" in place of "Enter" (seemingly no matter how I have rebound things) and that was a gigantic boon. Now it is just spamming "R" then "E" for those frantic scrapping sessions.
One thing I would very much like Bethesda to look at in terms of the UI is the change in player posture whenever you go into Dogmeat's special command dialogues (the ones that come up when you choose "Talk" and then "Fetch"). As far as I've found, whenever you enter this dialogue set (not sure if it happens when you select "Talk" or when you select "Fetch" but it is one of the two) even if you are crouched when you enter it, your character automatically stands up (and goes out of stealth mode). This caused me problems a couple times.
Overall, given it is a game that runs on so many different platforms and allows so many different user input devices, I think it is a pretty good balance. It could use a bit of tweaking here and there, but honestly I can see why there would be considerable inertia to make any changes at all. Any change they make at this point might well either cause new problems (either for all platforms or at least for some) and it would just as likely piss off a new contingent of folks who had adapted to the original layout!
It seems like a bit of a Catch-22 for Bethesda, so I cannot blame them if they seem 'unresponsive' to complaints about the UI.