First a few things to note: The shulker is alligned to the block grid, the NBT (aside from the position) doesn't change and this only affects shulkers riding other entities.
When spawning a shulker riding an entity, you can stand on it, and the momement is smooth, but the moment the shulker has been moved, the movement starts to jiter.
See the video for what I mean.
Nothing else is affecting the entity spawned in any way.
I also verified, no NBT changed after the teleportation, aside from the Z coordinate.
The function I use to spawn the entity is this:
summon minecraft:armor_stand ~ ~1 ~ {CustomName:'{"translate":"medabots_server:entity.balloon_bomb"}',NoGravity:1b,Invisible:1b,Marker:1b,Tags:["balloon_bomb","hostile"],Passengers:[{id:"minecraft:shulker",Silent:1b,NoAI:1b,DeathLootTable:"minecraft:empty",Peek:1b,Tags:["balloon_bomb","hostile"],ActiveEffects:[{Id:14,Duration:1000000,Ambient:1b,Amplifier:0b,ShowParticles:0b}]}],ArmorItems:[{},{},{},{id:"minecraft:diamond_pickaxe",Count:1b,tag:{Damage:3,Unbreakable:1b,CustomModelData:28}}]}
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This actually may just be resolved as duplicate; it seems that it's indeed the Peek value getting desynced, and refreshing it (setting to 0 and then 1 again) fixes it. The linked report has already been confirmed, got priority, etc.