I have no idea if this mod can support a mob with a complex nbt tag.When i execute the command
/summon spider ~ ~ ~ {Passengers:[{id:"minecraft:skeleton",HandItems:[{id:"minecraft:bow",Count:1b}]}]}
I can spawn a spider jockey,but i do not know what will happen if i want to execute this command in your mod.

so btw... Can you share us an example to use the nbt in MobStages?

MobStages has no NBT support. Commands will bypass the mod as well.