If you are going to give the phone away, logout your Mi account from that device first and then format data to wipe everything from the device, reboot twrp and transfer the stable rom to phone and install it.
Internal storage will be wiped completely, yes.
After format, and TWRP restart, connect your phone to PC and transfer the file to phone like you normally would. Then install rom .zip and restart phone to system and wait patiently.
I feel you man!
I have the same problem with my banking app called S-Mobiili (Finnish banking app).
I use device Kate (Redmi Note 3 SE) with current stable 9.5.4.0 which didn't solve my problem either.
I have a temporary fix for you:
Open Settings -> Advanced settings -> Accessability ->...
@ingbrzy will Kate users get 9.5.4.0 stable rom or is it going to be EOL too as Hennessy?
As a Kate user would love to get the update or I'm going to buy new phone if it's going to be EOL. xD
http://en.miui.com/download-301.html#449
https://androidfilehost.com/?fid=890129502657600172
or
https://sourceforge.net/projects/xiaomi-eu-multilang-miui-roms/files/xiaomi.eu/MIUI-STABLE-RELEASES/MIUIv9.5/xiaomi.eu_multi_HMNote3Pro_V9.5.2.0.MHOCNFA_v9-6.0.zip/download