Yes, a pop-up giving a warning would be good. It was a mistake not to do this for the 6.x Void storyline considering the importance of Cylva and Unukalhai and also how Gaia was left out until the very end in a single cutscene in which even she remarks not to leave her out of it next time.

For Crystal Tower specifically, I'm fine that it's forced since it'll also mean unlocking the Alliance Raids roulette for the player involved. The main reason why we all loathe CT raids is because syncing to 50 feels bad and then the lack of variety in the roulette itself because of the game not trying to promote unlocking content more, even when something like Ivalice is required before being able to go to Save the Queen areas.