Do the "Select Folders to Sync" and "Auto Sync" settings affect my to‑dos?

No. Those two settings (under Settings → Drive) control which of your files — notebooks and documents — are backed up to your cloud drive, and whether that happens automatically. Your to-dos are account data with their own switch (Settings → My Account → Data Sync) and sync regardless of which folders you tick. Folder selection and Auto Sync are still worth setting up for backing up your notebooks — they're just not part of to-do syncing.