I have not encountered the mentioned problems so far.
Ad 1. What security app you mean?
Ad 2. Correct I cannot find it either but it is not really important to me
Ad 3. Unknown to me
Ad 4. Unknown to me
Maybe reinstall the ROM once again. MIUI 9 is not available yet I belief for mipad 3
Did you follow:
1. Download en install ADB fastboot: https://androidmtk.com/download-minimal-adb-and-fastboot-tool or https://developer.android.com/studio/index.html#linux-bundle-size
2. Connect device to PC and wait until drivers are installed
3. Boot device in fastboot (Volume down+ Power...