Currently the Nextcloud client application does not allow to choose the download directory. The files are necessarily in an internal directory of the Nextcloud client application.
Personally I love Obsidian to take notes in markdown. I tried to create my trunk in the internal directory of the Nextcloud client of the application and as I could expect, I am not allowed.
I find it a shame that it is not possible to give permission to the Nextlcoud client application to write to a particular directory. On my computer (Linux Ubuntu), I can synchronize my files.
On the phone, I’m limited to one-way synchronization (upload). If I for example make changes to my markdown files directly on my Nextcloud server with my browser, I could see my changes on my computer but not on my phone. The Nextcloud client on my Ubuntu computer will download the new files but not on Android.
Syncing all the time can drain the battery quickly. But it is not mandatory to do frequent syncs. A synchronization on demand, or every X hours would allow to have files synchronized with its server and without draining the battery.
As a reminder, the Davx software synchronizes our contacts, our calendars every 2-3 hours by default.