Thanks again 😄 .... you are finding good points. Should have done that before v1.
I fear that this change are introducing breaking changes....well i will find out when i start aligning.

The reason for having this that way, is no reaason ^^....it's still legacy from the vuex-orm-next code base.

why does insert disregard relationships?

Dunno....well if i look at the code i know. This is legacy code.

why is it that I sometimes need to use query() and sometimes I dont? e.g. Model.query().where().get(), but also Model.where().update()

you are right i need here more silver lining. Although your example doesn't need query(). From my point of few i dont want to have repository all query functions, because it adds only not necessary code to the bundle. since most functions in repo are just shortcuts not to use useRepo.query()
UPDATE: After thinking i just add the missing ones into repository...because almost all are there.

why is it Model.save() but also Model.query().update()? Shouldn't there be a Model.update() as well?

well....yes....but right now update only works with query chain builder. So from that perspetive it makes sense not haveing it in repository.
actually it's fine because its aligning with https://laravel.com/docs/9.x/eloquent#updates . So you can use save() for update.
But including thrwoing an error seems to be something to have :)

why can I not use all() in a query like this: Model.query().where('id',id).all()? Either remove all() so that it's clear that that doesnt work, or make it so that it is similar to get(). (vuex-orm uses all() in queries, so this leads to a lot of bugs on my end)

well all() should never be the same like get()....otherwise i dont need all() at all. in the docs its stated clear that all() ignores alll query constraints. It also doesn't use the query builder. so it's also a performance difference. Maybe it makes sense to remove all() from query and move it to repository. This is sadly a breaing change.....seems i have to start on v2 ^^
all() -> get store results -> hydrate them
get() _> get store results -> execute query builder -> hydrate them