Ok, I think that I know why files loaded on a startup module are saved to the filesystem: because the FS plugin is loaded before the startup module is executed. This does not happen with boot.js, which is loaded far before than the plugin is loaded. Maybe the best option is, as Jeremy said, to write a new syncer module that tracks which tiddlers comes from files loaded from "remote locations" and which tiddlers were created within this TW. A task bigger than I initially planned I have to say.
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