For me the first time you flash Xiaomi.eu(assuming that you already use stock rom),should be like this, so it's 100% without garbage.
1)Make a local backup on the phone(not including accounts and some settings)
2)Copy the backup from /MIUI/Backup/Allbackup to my PC
3)Copy folder from the root folder to my PC. Folders like DCIM,Download,Music,Pictures....
4)Fastboot flash TWRP
5)Reboot into TWRP and allow the modification
6)Go to Wipe->Advanced and delete everything except SD CARD and USB OTG
7)Reboot again to TWRP
8)Connect to PC and transfer the rom zip file
9)Copy all the folders you have on your PC to your phone
10)Flash the Rom
11)Boot and setup the rom
12)Move using the file explorer the Backup folder to /MIUI/Backup/AllBackup
13)Restore and there you go... You have a clean install with all your data
*optional:
14)Reboot to TWRP and delete Dalvik and Cache