Sorry,
I probably don't understand what you try to achieve.
To my understanding ZPM is targeted to IRIS and its applications and
NOT to the underlying operating system.
- Though I admit that a lot of "hacking" into the OS is possible from IRIS. 

With the broad range of operating systems supported by IRIS, 
I rate this as a rather questionable approach, that I wouldn't support. 
 

My workaround was to place apt-get into Dockerfile as User root

EXCELLENT !   

there are 14 programming examples available in OpenExchange related to integration with node.js
https://openexchange.intersystems.com/?search=node&sort=d.desc

As iristrmd.exe only runs on Windows it is simply localhost:23  Telnet 
+ SMP:  System > Security Management > Services > %Service_Telnet enabled

iris session is not available in Windows

I use Putty for years. Always working fine

Right. It stands at the first line and  <ctrl>+<F5>  in Studio starts it

It is also in Debug  menu / Go 

I think that the design idea was to have a last chance to set breakpoints.

just tried to reproduce a similar case in Terminal.
#0) clear all stored  breakpoints (menu: Debug / View breakpoints / remove all)
#1) set the breakpoint in Studio using F9
#2) attach to process (shell if in Terminal)
#3) do ^yourroutine in terminal
#4) In Studio: <ctrl>+<F5>  let it run 
if your breakpoint is reached you see the yellow box

Hint: try it with some simple 5 line routine first

If you never see the yellow box then you just don't execute this line 

That's correct if you are already in an .int routine.
OTHER relates to cls, mac, ..... 

As an add on:
If you also want to get back the result of your command you may use CPIPE device.
See my article and the related example in OEX  and this fresh one for Python 

Ahh!
Studio debugger is based on ZBREAK command.
old style BREAK is only useful for interactive debugging in the terminal and ignored in background
I always tried not to mix it up.  Not sure if this is the reason. I think it's suspicious. 
 

I've seen such behavior during debugging when I fell into some deployed system code (.obj only)
A similar effect happened to me when I touched some customized command, function, variable from ZLANG***
[which I tried to debug !!!]

I could gain control again by some <SHIFT><F11>  until returning to some code covered by .int
As Studio stores a lot of info in the Windows registry just killing Studion might cause some confusion. 

Could you pls. be a little more precise about what you expect:
heavy & complex & simple is quite ambiguous.