It would not be there unless you put it there.
If you create it as a User Setting, though (on the Settings tab when you update a User), it will not be in the Profile. It is available like this:
$treeRootId = $modx->getOption('tree_root_id');
The User Setting will override the System Setting, but only if the user is logged in.
More important, tree_root_id is deprecated and ignored in current versions of MODX, though you are free to create it as a User Setting or an Extended Field in the Profile and use it however you like.
I would probably use a different name, however, in case some add-on developer decides to use that one. There are some examples using tree_root_id in my book (written before it was deprecated) that may give people ideas.
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PLEASE, PLEASE specify the version of MODX you are using.
MODX info for everyone:
http://bobsguides.com/modx.html