Mod settings are read-only through the Lua API. My mod setting isn't changed, but some mod must have some code that explicitly reenables technologies whenever some event happens (probably on_configuration_changed). After all, the recursion technologies are only hidden from the tech tree and not completely removed (because per-map settings are way more convenient than per-launch settings, but only per-launch settings can actually delete technologies), so other mods can in theory hop in and do their own showing/hiding.