Applications are agnostic to which filesystem storing the files.
I understand your issue as a navigational issue - so my first question is - how do you mount the partitions?
Are you mounting them on the fly from a file manager or do you have setup permanent mount points?
If you are mounting on the fly using a file manager - mount will reside in /run/media/$USER/device-uuid-or-label and only be available to applications such as qpdf or intellij if you previously mounted the device using your file manager.
If you want to be able to access the partition without having to mount it beforehand then you will need to set up a permanent mount. This can be done using either fstab or systemd mount units.