On your second question about different loops. First, you can loop through any register via (dec <reg>; jnz <label>), thus having nested loops. Second, all valuable registers are pushed onto the stack and popped before/after a call or an interrupt, so their contents don’t change. Some registers have to be saved by the caller and some by the callee, depending on a calling convention and an actual usage. The stack is always available (rsp points to its top), so you can offload temporary values and concentrate on current evaluation, loading values on demand later.
It’s sometimes difficult to think about the assembly code in situ when you start to think about the operating system doing a ton of context switching and paging etc. in the background, which can distract your thought process from what’s right in front of you (as well as the operating system’s software interrupts / system calls on top of the basic ISA, which is another abstraction!)
Older systems had the currently running program as the entire context of the system at that point in time - in a similar way to embedded programming, which is imho a much easier realm to learn assembly in once you’ve got a bit of basic electronics under your belt!
Even in those "old" systems of single address spaces and no protection, you're constantly getting timer interrupts, interrupts for I/O, etc., which your application might not have installed its own handler for.
I suspect we’re both making a similar point in a roundabout way - the operating system is both another layer of abstraction on top of the Instruction Set, while also making the programming process for that chipset somewhat easier (providing software interrupts etc. at the expense of bare metal understanding).
My argument is loosely that modern (x64) assembly is not so much targeting hardware as it is programming into a software abstraction (the operating system).