How can I get warps to save properly?
By default, warps will save when you stop your server. If you kill the server in a non-graceful fashion, they won't save. Don't worry, there are ways around this. The easiest way is to boost the storage-mode setting in the config.yml to either 2 or 3. There is documentation in the config file about what each mode does.
What is weak positioning? Does it impact performance? Can I disable it?
Weak positioning is convenience hack. It allows SimpleWarp to reference a position on the server with only the level name and not the level itself. It has a marginal impact on performance because the level object needs to be fetched on demand instead of being stored in the position object. It can't be disabled as disabling it will cause a bunch of undefined behaviour.