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comment Is modern encryption needlessly complicated?
You ask: If we have a secure channel to communicate so we can agree on a one-time-pad, then why bother? One reason would be faster exchanges. I worked on a system where relatively slow HTTPS is used for the initial account/password exchange to establish a secure channel, then much faster encrypted UDP is used for subsequent data exchanges at very high volumes and frequencies (at speeds HTTPS could never keep up with).
comment Do these 2 KSA shortcuts weaken RC4?
You ask if Alice is sending a separate array for each message. Just assume she's sending the array as frequently as she would be sending a new key. The point is not how or how often they are managing to securely exchange a key, the point is can't Alice simply send the array instead of the key so Bob can skip the KSA? As for the swapping, I've fixed the pseudocode.
comment Do these 2 KSA shortcuts weaken RC4?
Re Shortcut 2, you ask "how cryptographically secure" the OS function is. The standard KSA swapping seems pseudorandom at best. If random() is "only statistically random", isn't that still at least as good as the standard KSA swapping? If a func like random() is used to scramble the array, what subsequent test could be used to determine the result is worse or better than the standard KSA swapping? Or, what's a known random() func that would be at least as good but possibly simpler than the standard KSA swapping? Is the standard swap trying to do something other than randomly scramble S[]?
comment Do these 2 KSA shortcuts weaken RC4?
I think your concern with Shortcut 1 missed the point. Regardless of how many times they use the same key or switch to a new key, the question concerns sharing the precomputed array instead of sharing the key. Is it not true that giving Bob the array is equivalent to giving Bob the key, and Bob then doesn't have to compute the array? Any time you want to give Bob a key, how is it worse to give him the equivalent array instead?