Well, you've nailed our scope - we do tend to focus on the more theoretical side of crypto.
That said, it's not always that clear where the boundaries lie - what sounds like a software question might actually be a perfectly fine "implementation" question here. Often, when asking a question it's hard to know - because it's easy when you understand the material to know what the scope is, but if you knew, you wouldn't be asking the question in the first place...
Your existing questions seem fine to me. I don't want to discourage questions; the worst case scenario, if they're well asked as yours are, is we ask for clarification and/or move it somewhere else.
I think when it comes down to it, if you're looking to understand the implementation of crypto specifically (and possibly questioning the whys in existing implementations) you are in the right place. If there's any you want me to look at, feel free to grab me in chat. Every question we look at and move/don't move is an improvement to understanding our scope.
Perhaps this might be a useful set of potential questions I think involve software but would work here. Might make more sense than the above!
- Efficient implementation of RSA in software - how does the CRT technique work (asked recently, but not with this title).
- How do I generate a random prime such that users do not end up with the same private key? (think we might have covered that)
For more examples, implementation might give you a flavour.
Finally, note we also have some other sites on the SE network which might cater to this kind of question:
- Stack Overflow - covers programming. "I am trying to use .net's crypto api, it doesn't work, what am I doing wrong?", "I've implemented AES like this but this Xor here is giving the wrong value, why?", and so on. Questions that need a programmer to answer.
Security.stackexchange covers implementation aspects of crypto too, as well as security platforms in the wider sense. The community there is likely to advise you to do the "right thing" security-wise and will focus on all aspects of security; here, we assume you want to know about crypto specifically, and we assume you already understand the risk in deviating from known implementations of protocols, where that applies.
For more on this, see how to decide between Cryptography.SE and Security.SE?
- Programmers.stackexchange covers conceptual questions on software development. So if you're looking to understand how to go about more general designs and abstractions, this is the place to go.