I type something in the console window, like 'automaterial 1', to turn that feature on. Instead of it turning itself on at startup.
That's not appropriate for instance for some things like autosyndrome or steam engine, which provide functionality to support enhanced raws. A steam engine workshop without plugin support behaves wrongly in a very unintuitive way. What they should be doing (and steam engine actually does) is check once on world load if there is anything in the raws for them, and if not, do absolutely nothing until another world is loaded.
It is also silly to clutter up the command list just so that something can be enabled or disabled, so maybe we need a centralized enable command that can contact the relevant plugin. There is also an issue that users don't read readme, so authors of things like LNP or mod packs are quite likely to include a config file that enables everything anyway.
Regarding automaterial, since falconne initially distributes his plugins separately, they tend to assume that if they are installed, the user surely wants them to be active, even if they aren't just adding something rather non-intrusive like a hotkey to activate dwarf manipulator in the unit list screen, or even search prompts.
Eventually, the most basic problem is there is no viable universal configuration system in dfhack, and every plugin has to implement its controls individually as it sees fit; and developers tend to assume that everybody wants their thing.