The ODM query builder supports atomic update operators, but does not support passing an aggregation pipeline. This could work like this:

$builder
    ->update()
    ->field('id')->equals($id)
    ->pipeline()
        // Same syntax as aggregation pipeline builder follows here

We need to evaluate whether it's feasible to use a fluent syntax here, as we likely won't be able to reuse the full ODM aggregation pipeline builder as the execute methods would conflict.