Unfortunately I never worked with a qnap, so I can only offer best guesses.
It looks like ownCloud comes in a docker for qnap. For dockers it is quite usual to have an external nginx/apache/… performing the SSL termination and proxying plain HTTP to the docker port (in the appliance). Are there any settings in the frontend to accomplish this? Maybe this is an option for you? In this case you shouldn’t have to import any certificates.
FYI regarding the multiple occurrence of rootcerts.crt, the one in the files_external folder is shipped with ownCloud itself, the one in the files_external/upload is the one imported by you.
I admit, the documentation available on the web on both the qnap and the ownCloud side is very poor, especially when there was this big press release back in 2020: QNAP Systems Inc. and ownCloud GmbH announce strategic partnership - ownCloud
@dmitry I see there is some documentation at ownCloud on QNAP :: ownCloud Documentation but this does not cover any certificates at all. Do you know some “insider” who could add the relevant lines? - or - is this as @anon21401411 wrote at [1] that “i think the Qnap NAS app isn’t provided by the ownCloud people so this could be the reason why no one was able to answer / help here yet.”