The PVP designers are completely separate from the PVE designers, with one noteworthy exception. The PVP designers are required to listen to the PVE team and incorporate important pieces of the class into the PVP design. This is why DB and DP have been in both PVP summoners. Otherwise they make a massively simplified version of the PvE rotation balanced around both a limited set of skills and maximum class theme. This is also why the current PVP SMN has Aetherflow, Trance based on spending Aetherflow stacks, and still has DoTs that seriously feel terrible to use and WHY ARE THEY THERE PVP DEVS?! But they got rid of the egis, which weren't there in SB either, and as such don't have egi assault.
All of these factors combine to massively streamline classes, and this is why a 3-step combo is on 1 button in PVP instead of on 3 separate buttons like it is in PVE.
It just so happens that a lot of really good design choices are made by the PVP team in their "simplification" of the jobs that would have made a lot of sense if the PVE teams did it as well.
I disagree, but mostly because this type of forced desync is something every job deals with to some degree. Cooldowns being forcibly held by boss mechanics isn't something new, and it just means you come in swinging once the boss drops again. From Trick Attack to Drill to Ley Lines, there are very important mechanics that get held up. Hell, I've seen transitions as a MCH make it so I had to delay Wildfire because the timing just wasn't right. This is normal.
SMN is unique in these problems in that it has not one, but several core mechanics that can be screwed up by boss jumps that, once desynced, basically cannot be synced again because too much damage is tied up in them, meaning you have to keep them rolling but it doesn't feel very good forcing them, especially with how bloated the class is and how often it has to constantly be pushing buttons.
If you made it so only Trance was your delayed mechanic, then it wouldn't matter half as much because at least it will be consistent about it, and restarting the rotation from there, while not fantastic, at least isn't awful. But none of that matters right now because the class is a hot mess to handle as is.