I have used the updater app since I have this Redmi Note 2 Prime, no problems whatsoever.........!!!
So, how can the updater app do a good job? Actually I am curious too as to why we are supposed to use TWRP to flash the new roms. But I'm just a noob, so I am surprised as well.....
For my device, updater is recommended ;
For some other devices, other means are recommended.
I remember reading something about signature problems or something like that...
But you're missing the point - translators ask to install using specific different method for a reason, obviously ;
Might not be a reason that affects all devices of a type, but it must be needed for some, so for safety and simplicity they ask it for all.
But stubborn people sometimes keep going around the recommendations, or simply don't even read the opening post... and some of them then have problems, and come here crying that their device is broken and asking for help... And for me, that's wrong.
If I would be doing a piece of software for free, with specific indications of how to install it, and then some individuals whom had install it differently would come crying to me that the device doesn't work... I would send then to take a walk, at the very least.