You're pretty much on point. When designing a scheme, whether a low-level cipher or a higher-level protocol, only a small fraction of the time is spent on the initial design itself. That is not to say that a scheme is designed and promptly finalized; analysis results feed back into the design process, of course. But the analysis is generally by far the most time-consuming task.
Additionally, sane people do not use building blocks that they don't trust. If you need a block cipher you use AES (which is partially backed by security proofs) instead of designing your own (unless you have very specific requirements). This saves immense time in both design and analysis. Same with modes (Feistel structure, Sponges, HMAC, etc). Proofs play a big role here, although it is important to understand what they say, instead of blindingly assume they mean whatever you use them for is secure.
You are right that implementation is generally left as an afterthought. This is slowly changing, and primitives are increasingly being designed for implementation and side-channel friendliness.
Additionally, sane people do not use building blocks that they don't trust. If you need a block cipher you use AES (which is partially backed by security proofs) instead of designing your own (unless you have very specific requirements). This saves immense time in both design and analysis. Same with modes (Feistel structure, Sponges, HMAC, etc). Proofs play a big role here, although it is important to understand what they say, instead of blindingly assume they mean whatever you use them for is secure.
You are right that implementation is generally left as an afterthought. This is slowly changing, and primitives are increasingly being designed for implementation and side-channel friendliness.