I think there is a better way, see https://github.com/symfony/symfony/pull/29010/files#r229492831

@ogizanagi see my comment linked above. I don't think we should follow this path.

@nicolas-grekas : Continuing the discussion here, as it's seems more scoped here.

all this logic should be removed: ChildDefinition already have their merging logic. Overwriting an existing parent argument is done by using index_0 as a key. Let's make things simpler by reusing existing knowledge.

The current logic typically allows this: https://symfony.com/doc/current/messenger.html#using-middleware-factories
Unless I miss something, your suggestion will require writing:

# config/packages/messenger.yaml
framework:
    messenger:
        buses:
            command_bus:
                middleware:
                    - doctrine_transaction_middleware: ['index_0' => 'custom']

to change the entity manager name.

The idea of such factories was to expose simple config for middlewares. Not leaking Symfony's DIC specificities into it.

But actually, I'm not fan of this PR allowing to replace any argument by index through the config, just for fixing this issue.
The middleware factory args mimic defaults in a PHP function. I.e, given:

function foo($bar = 'foo', $baz = 3, $qux = null);

either you're satisfied with defaults and use foo(),
either you need to change a value, i.e $baz and use foo('foo', 5), not foo($baz=5). And it's fine to me here.

So about this issue, I'd suggest a more pragmatic approach: #29038

👎 let's kill these workarounds on top of hacks. We need to play by the rules of the definition inheritance, not against.

doctrine_transaction_middleware: ['index_0' => 'custom']

nope: my suggestion is to make doctrine_transaction_middleware: ['custom'] work.
This can easily be done by playing the rules of definition inheritance: the bus name should be undefined in the parent definition, and be the first next argument in the constructor definition.

Already fixed in #29010 (comment) by removing special edge cases, instead of adding more ;)