QNAP designation of MinimServer as EOL

[Klaus57]

As mentioned, the final decision rests with QNAP, in line with their strategy to move away from native applications. Also the discontinuation of JRE support—as I understand it—is part of this approach.
The rationale is that each Docker image includes its own, perfectly tailored Java Runtime Environment. This eliminates the need for a system-wide JRE installed via the App Center, which could otherwise lead to version conflicts.
In QNAP’s own words: “To ensure system security and optimize performance, QNAP will discontinue support for JRE in the App Center. Users are encouraged to migrate Java-based applications to Container Station.”
I don’t believe this is just "empty talk," which is why I suggest that a "Plan B" should involve Docker. The issue you raised regarding read/write permissions is certainly solvable; there are already applications on QNAP systems that are provided exclusively as Docker containers—for example, SongKong for QNAP NAS. That application also requires the entry of a license key.
Lastly, the final say on MS rests with you; I have simply shared my own personal opinion.