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Fluent standalone means you lose out on the WB workflows (ie parameter managers etc) but gain flexibility to launch from and save into different locations using paths with filenames of your choosing. Both are "best" but it's for the user to decide which features they want. Note, the lines will blur further with all the tools going into Fluent and Optislang links etc so expect the above to change in the future.
GUI journals are often problematic. If you launch the journal with a panel open but recorded with it closed the journal may fail or do something weird. We recommend using TUI journals, ie
/file/read-case mycase.cas.h5
/file/rc mycase.cas.h5
are the same command: build the commands from looking in the TUI, Enter accepts a command and will list the options in the new menu level, q (Q) takes you up a menu. Always use the full path and / to force the full root level command. That also stops the command going wrong if you're in the wrong menu level. Also test the journal on a small case.