I find those about as dissonant as contrast between servants' relations scene, many light hearted in nature, and the main story itself.
In regards to tonal dissonance, i simply disagree with you, particularly in regards to later chapters, putting the story quality aside.. That is, majority of things you describe as tonal dissonance that breaks the flow, i dont find it as such.
For example, Blackbearf is a real hit and miss, in that some people actually like how the whole Oceanos is not meant to be completely serious to begin with, but a fun adventure story, in which case Blackbeard actually helps strengthen the mood as opposed to breaking it. Understandably, some people would dislike it but again, personal preference.
While i would admit some of your points due to personal subjectivity and not everybody would think the way i do, especially in regards to older chapters, i find people doing the same on later chapters to be more of a nitpicking and them exaggerating it. Thus overblowing it or just downright blindhating it.
The fact that some people hate the media and then trying to hate the story as well in a, pardon, hypocritical way does not help my impression in that its simple hate justification.
Thats not to say that FGO story is the best out there. Its indeed sometimes lacking, verily so in some older parts. Or just downright bad.
But i cant help but to find many points to be nitpicking the story just to fuel the dislike not on the story itself, but on the medium.
I have no problem people disliking fgo.
I just have problem when the expression of such hate is misplaced.