This kind of thing is unfortunate, but I don’t think we need to be too concerned about it. Eventually, the tooling will make this a bit easier, and for now it seems sufficient to me to use these command line flags at the top level for "Hello, World!" type scripts and during prototyping, and also module-level options where that makes sense.
I’m currently trying out this idea of launching one script with the flags for setup-type stuff and then calling another julia process without those flags inside. I’ll report back once I’ve worked out the kinks 