Credit card apps and rooting

I am not getting a clear picture whether it is possible to have an Android smartphone rooted and use credit card authorization and bank transaction authorization apps, especially under newer Android releases.

Obviously many credit card and bank apps authorizing transactions try to find out whether the device is rooted or jailbroken. If it is they refuse any action. I actually understand this, as security-wise these apps were planned to be a completely independent second factor - like purchase transaction executed on a PC and transaction authorized on the cell phone. A hacker would have to have hacked both devices at the same time - almost impossible. They see the risk of having the Web transaction executed on a rooted and in the following hacked mobile phone and then getting the fraudulent transaction authorized from the same rooted and hacked phone.

What I want to achieve: I want to be able to delete bloatware, plus in remote access through USB or Bluetooth I want get write access to folders owned by app users, for instance to move a GPX file into the Tracks folder of a navigation app. I am OK and would even appreciate if any such actions require temporary Super User through user interface (UI) interaction.

I do not intend to completely replace the operating system or remove all Google apps. I also do not want to loose automatic OS and app updates and run into the hassles of manual updates and incompatibilities of some custom ROM. I do not want to spend additional time managing my phone. I do not want a malware infected downloaded and installed app to be able to silently access any security-relevant transactions on other apps. I still want to use credit card and bank transaction authorizing apps and be sure these still work after the next Android upgrade.

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