I think what you're saying is that you have a factory which is a singleton and you want it to create new objects of which you want a new one each time with full dependency injection. The old way of doing that was Method Injection which you link to above. The new (and arguably cleaner way) is to use a Scoped Proxy.
You can either use annotations or regular config but the idea is that you create a proxy around the bean (e.g. The InnerObject). When ever you need a reference to it, spring will automatically provide you with a new copy with the appropriate dependencies inserted.
1 It turns out that this doesn't actually work for prototype beans. It did however lead me to method injection, which solves the problem - not quite as cleanly, but still nicely. Thanks dough – idbentley Apr 14 at 18:29.
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