Just FYI it is recommended to run twrp and su. Regarding you question: can you use the functionality that requires root in the apps you mentioned to be working? If not you simply have no su access at all. In case you can run them go into the su UI under settings and see if you can manually grant su permission to TiB and the like. It seems strange to me that super user should only work for some of your apps. I might be wrong though, I'm no expert.
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