I remember needing to learn Ruby and Rails on an existing closed codebase and having the debugger take me right to the core of Rails several times to understand why certain things were done in a certain way in the top level code. This allowed me to get acquainted with internals of Rails and how Ruby's inheritance system much faster as well as the existing codebase that was built on top.
That's the theme I hear when prodding people who (sometimes loudly) say they don't use debuggers. They work on codebases that are either small, solo projects, or change very slowly. That way they can keep an accurate simulation of the entire program in their heads.
Meanwhile, I've always worked on codebases that were changing faster than I can keep up. The majority of my debugger time has been in code I've never seen before.
I don't find it a hindrance in any way seeing what part of the Django code called my code.
Understanding the code is often a luxury we don't have, either because we didn't write it in the first place or because there are just too many moving parts each tracking their own state and interacting with everything under the sun.
This is especially true for long-running programs that do much more than just transform inputs into outputs. For example a video game would be complete hell to develop without a solid debugger. Even if you believe you understand the complete code and all its behavior the testers will always find a way to make the game crash after 2 hours of playing leaving the game's state completely broken and without a debugger you'll be scratching your head endlessly trying to replay how that happened.
In these cases the number of different states and behaviors you can get out of the system is incredibly high, easily a few orders of magnitude more than the human brain can handle.
For me at least, that's typically my cue to start refactoring. If I can't model at least the general behavior of my program in my head, then it's probably needlessly complicated.
This isn't always possible, of course (such as in the case of long-running programs, as you mentioned; it's still possible in a lot of cases, though, and splitting off functionality into smaller, easier-to-digest pieces can make troubleshooting much easier), but it's been a useful mentality for me, and has significantly reduced the need for me to use some sort of debugger or even 'print' statements to make sense of code.
This doesn't address the original question of understanding new codebases, though.
The debugger runs in as many threads as the app itself. If you're debugging C#, and your program is in 37 threads, you can debug all of them simultaneously or debug one and ignore the others.
Understanding the code and keeping it in memory sounds like a great practice, but it also seems entirely orthogonal to using a debugger.
I have the exact opposite attitude: I live in the debugger. Most of my resistance to trying "new hot" languages is their universally terrible debuggers. (Usually they either don't exist at all, or only exist in CLI form.) IMO, if you don't have a working, stable, graphical debugger, your programming language has no business being 1.x.
If you're working on, say, a huge Java codebase, then a debugger is practically essential because you've got a lot of code to navigate, and you probably want to see what flavour of objects are being passed around and how their state is being updated.
On the other hand, if you're working on, ooh, a Nodejs codebase, you're probably looking at less code, with a debugger that's much slower, and probably more functional code that is operating on data directly. Using a debugger in that case is often slower than just using print statements.