As the title clearly describes, some UTF-8 characters such as (ğ, ç, ş, etc.) could not be displayed on the console output despite (1) setting all the encoding preferences available in the Settings UI to UTF-8, and (2) adding the -Dfile.encoding=UTF-8 parameter to the idea64.exe.vmoptions file as it is provided in another question in Stack Overflow.
IntelliJ IDEA Version: 2018.3.5 (Ultimate Edition)
Edit: I am running my web app in debug mode, and using Apache Tomcat as the servlet container. So, the console output is the log of the web app.
As @Andrey stated, if you want to see those symbols in Run/Debug console you should add
-Dfile.encoding=UTF-8VM option to your Run/Debug Configuration, not to IDE options.