Mark already gave some good answers. I'll just fill in a couple of blanks.
I should point out that I will mainly talk about RSX-11M-PLUS here. There are some differences in RSX-11M to what I'm saying now. And if someone really wants to know, I can explain those. But I would in general recommend people don't run -11M. It is just more limited, and a little more cryptic and difficult to deal with. But mostly same or similar.
First of all, as mentioned, LB:[1,2]STARTUP.CMD is run when the system boots. It should normally have installed PIP already. If that isn't the case, then either that execution was aborted, or else someone have modified the file. If it's been modified, who knows what your system looks like, and it can be tricky to use the manuals, since they do assume some sort of standard initial setup have happened. And if it wasn't allowed to run to completion, please reboot, and answer any questions it pose, and let it run to completion.
It's incorrect that [1,54] are privileged task, and [3,54] unprivileged. There is a distinction between what is in the two directories, but for normal users it don't really matter. But programs in [1,54] are closely tied to the running kernel, and if you build a new kernel, programs in [1,54] might need rebuilding too. Programs in [3,54] do not. In RSX terminology, they are vectored.
Now, I did say "might". Some programs or binaries in [1,54] might not need rebuilding anyway, but it is more of a thing depending on multiple factors.
Accounts and directories are not the same thing. Also, users sortof always exist, even if no account for them exists. This might sound complicated, but isn't, really.
So, let's go through the different things one by one.
First of all, directories do not necessarily have any association with a user. Of course all files (and directories are just files) have an owner. But the directory name itself is either in UIC form ([group,member]) or named form ([name]). If in UIC form, it just means that you have two numbers for specifying the directory. Such a directory can also be referred to in name form, in which case you just take the three octal digits that makes up each part, and put them together. So [1,54] is in named form [001054]. A few UIC form directories are special, in that the system have some expectation that they exist, and contain some important files. These directories can be set, so they are not hardwired as such. But they are always in UIC form. But there do not have to exist any users with the same UIC, nor do the owner of a directory have to be the same as the UIC name of the directory. But it's important to understand that just because some UIC exists as a directory, that do not necessarily have any implications about existing users or anything else.
Second, terminals are always associated with a UIC. And now we talk about UIC as a user, not a directory. This UIC is called the protection UIC, and it governs what you have access to. This is matched against the owner information in files, and in combination with the protection fields of a file tells if you have access to that file or not. Same thing with some other resources in the system, such as common regions. (In addition, if the group number of your UIC is 10 or less (octal), you are considered a system user, and the system file protection field will also apply, and you are also always allowed to do things like changing the protection of any file, no matter what the current protection mask is.)
In addition, a terminal have a default directory. This default directory is just what it says. It just tells which directory any file operation will work in, if you do not give a directory specification for a file. You can obviously change your default directory at any time. And you can change it to any directory (or UIC), even if such a directory do not exist. It's just a string (or a number).
Also, each terminal have an attribute, telling if that terminal is privileged or not. If it is privileged, the user at that terminal can change his UIC to anything. It don't matter if that user "exists" or not. As I said, all users exists, in a sense. A privileged user can take on any identity.
Finally, there is the accounts database. In there you have "existing" users. There are account you can log into on the system. But in order to log in, the terminal have to be currently logged out. At startup, unless the STARTUP.CMD file logs the console out, the console is left logged in, with the terminal set to privileged. So you can do anything from there. You can of course log the terminal out yourself, and then the console can be used to log in to the system, just like any other terminal.
Now, when logging in, the login process will check if the group number of your UIC is 10 or less (octal), and if it is, your terminal will be set to privileged. And otherwise your terminal is set to not privileged.
Finally, within the RSX system, there are some conventions for UICs and directories, which can be helpful to know:
As mentioned, with users, a group number of 10 or less (octal) is a system user, and when logging in gets a privileged terminal. Such UICs also match against the system field for file protection.
When it comes to directories, you usually have:
[1,1] system libraries
[1,2] help files and system wide command files
[1,3] directory where lost files are placed
[1,4] system log directory
[1,6] print and batch queue directory
[1,54] system image, drivers and tasks dependent on current system
[2,54] baseline system
[3,54] system tasks and tools
[6,54] standalone brusys
[11,*] kernel, drivers
[12,*] MCR and related tools
[13,*] MOU/DMO and some more file system control stuff
[14,*] RMD
[15,*] Executive utilities
[16,*] Multi-user tools
[17,*]
[20,*] File related tools
[21,*]
[22,*]
[23,*] DCL
[24,*] TDX
[25,*] QMG
[26,*] BPR
[27,*] CON,HRC
.
.
.
[*,10] source files for parts of the system
[*,24] object files
[*,34] list files
[200,200] SYSGEN
Group 5 is usually used for DECnet related things. Group 4, 7 and 10 are usually not used by anything. I usually create privileged users in group 10, and use directory [4,54] to add local system tools so I don't have to pollute [3,54] with that. And then add unprivileged users in group 201 and onwards. But of course, now we're really talking about local conventions...