This is not at all related to GApps.. reflash you trwp..openGAPPS PICO/ARM64/6.0 (from 4 March 2017 - 22 March 2017 Size: 75.78 MiB) induce bootloop in Xiaomi Redmi Note 3 Pro (Qualcomm).
In previously versions (PICO/ARM64/6.0) size been ~100 MiB and all was normal.
logs in twrp: not mount /system as before versions, only mount /persist.