Several important Story Triggers do not work when riding Merulina.

[Seralyna]

Several important story conversations will not play while riding Merulina, alongside that important triggers will just not play. The most egregious of these is during the Mandatory quest 'The New Strange' , Where a line from Ordis is required to be able to scan Chroma, and end the mission. If you miss it, the mission is incompletable. 

Another example that is less progression blocked, but also important is during the quest 'The Second Dream.' During leadup to the main cutscene of the final mission of this quest, several whispers of memories will play, unless you are riding Merulina, in which case they will be entirely skipped. Even worse, when you do finally reach the cutscene trigger, it will play normally, but after the cutscene ends instead of Carrying the body as you should with reduced movement, you instead have full control of Yareli, admittedly with some physics glitches that go away when you mount Merulina again.

I personally tested The Second Dream several times, and when progressing normally as Yareli (or any other character) without Merulina, the voice lines play and the State of carrying the body is entered normally. I even tested riding right up to the cutscene trigger and dismounting Merulina right before it. In this instance, the voice lines did not play, but the events following the cutscene play out normally.

I suspect many other missions have at the very least minor voice lines that don't trigger while riding Merulina, but since this is my first time playing through the game it is hard to be certain. At least one other instance happened when playing the Quest 'Natah.' My friend commented on hearing a voice line referencing the name 'Natah' for the first time, which I never heard.

Attached is a screenshot of myself riding Merulina (with a gun out) while a voice line from Lotus plays that should normally only show up during the scripted Body carrying sequence.