Really long title, but I think it has what you're asking for
"Practice of Cloud System Administration, The: DevOps and SRE Practices for Web Services, Volume 2"
This book takes a vendor-neutral look at architecting and managing distributed systems, so it naturally speaks in theoretical terms, but with a practical path to success. I'm not sure it will address everything you're curious about, but it will get you a long way for sure, and I'd recommend this read to anyone from an Administrator, SRE, to even tech management. I have to give props to TutoriaLinux on YouTube for the recommendation as it came to me!
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On a more generic note, I don't think it's possible to learn every finite detail, though I maybe correctly understand why you're posing these questions as examples. I think it's interesting to think more broadly, such as considering a user's workflow when developing software or a platform, rather than to drill in on when to use a VM vs a Container. Find yourself some guiding principles and apply those to your learning, methodology, implementation, etc. and I think you'll always head down the right path. To that end, it might be worth reading some of those principles. I take time to review my principles yearly to keep a strong mental framework for when I'm deep in SRE work.
I'm curious to hear if anyone else has some recommendations along these lines.
I'm a big fan of the book The Practice of Cloud System Administration.