Maybe a Side Content Warning...?

[Jeeqbit]

The fact they can't reference or outright include characters and events from side content in the main story severely limits their options and just leads to bizarre moments like only getting the option to tell Zero about Cylva long after we've left the First, it sucks.

Typically, things like this are minor and they don't make them a big deal. Yes, for those of us that did the storyline with Cylva, it's been exciting every time there's been a relevant update, such as the update to the Warring Triad and the MSQ looking more into the 13th, but it is ultimately minor and only intended to satisfy the excitement that sidequest players would feel, without affecting MSQ-only players.

Unfortunately, making the Crystal Tower Raids mandatory back in 5.3 was (apparently) so badly received

No, it was not badly received. In fact, players petitioned for them to make it mandatory because it wasn't, and they merely complied with that popular request.

The reason it was not badly received was because we always got Crystal Tower in the Alliance Raid roulette prior to that change. It didn't fundentally change anything about that, because it was always the most common one to get. Regardless of whether it was due to 1 out of 24 players being below level 60, or due to people intentionally reducing their item level, Crystal Tower was always the most common then.

they swore they'd never do it again

If they swore they would never do it again, then I did not see where they said this. Rather, they were reluctant to do it in the first place, which is why they didn't do it to begin with. However, they couldn't deny its fundamental relevance to the Shadowbringers story, so they gave in that one time. It's unlikely they would do it again, but it's not impossible if there is some side content that they later want to build the MSQ around.

Most likely another reason for the delay though, was that if they put an extra requirement on completing Shadowbringers on release, their support desk would have been overwhelmed with confused players that don't know how to find or do this sidequest and they dodged all that.

They could just include a pop-up

They could and maybe they will. They have added popup QoL recently to explain certain other things (and it's retroactive), such as invisibility in society quests, running with an object, NPCs following you and things like that.

[Alicie]

No, it was not badly received. In fact, players petitioned for them to make it mandatory because it wasn't, and they merely complied with that popular request.

It was very badly received, nobody was happy about few extra hours of mandatory boring story slop