if i understand your question properly (and forgive me if I don't) you're asking whether or not it's better to have multiple objects persistently stored seperately or one tree object stored by itself.
I think that aside from your own stylistic preference, the only difference I can think of is that, if you store multiple objects seperately, and need to make calls to all of them, you may take a battery hit as going to disk is costly. Having one object requires just one call, which is lest costly.
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