Well, for me I find Your Lie in April to work fine, because although it does shift between the serious moments and the comedy quickly, and it can sometimes be jarring, it does seem to basically be following set rules (it probably helps as well that the comedy is actually funny, unlike in Amagi where it's pretty dreadful). It's exaggerated, but the characters are still reacting in a straightforward enough manner.
Yeah, Amagi plays things straight, but it's almost playing things too straight. That's part of the reason the Sento stuff bugs me, because the basic tone feels completely out of proportion to the whole 'magic fairies running an amusement park' thing. The stuff with Latifa mostly feels keeping in line with the show, but Sento's story really feels jarring. I also don't feel like the show actually does much with her character in the fourth episode. It still feels like she's basically playing a trope, and the scenes kind of feel like they're just following along an exact script for 'the person who doesn't really understand human interactions so has trouble dealing with people's issues'. This is kind of why the tone bugs me. It feels like a whole lot of different things thrown into a blender ('whimsical storyline with magic fairies saving a location, 'wacky comedy with two characters constantly fighting and getting shot by a magic gun', 'serious melodrama about a solider who can't integrate with the rest of society'), all of which is handled in a mediocre manner and none of which really seems to click into place.