I think this is something realy cutomer specific.
It depends what kind of information you want to query for in regard of information reuse.
e.g. you store a specific number from your plm system visible into a udf to be able to find this specific line item for reuse or modify. ... or you want to create reports based on some informations in your line items ... in that case you can store them also into the udf's and reuse them for some queries. ... Or an ordernumber which comes from a diffrent system but has to be published to better find this lineitem to work on it. (if more departments work with the same line item)
I believe the UDFs do show up as properties on top-level (or you might have to create similar named properties) but it is possible to assign a value to a UDF property at run time and you will notice that the lineitem now shows that updated value. Typically, UDF values can be used for summary information like cost, price or a general status of the model associated with that lineitem (other than the basic status provided by base Rulestream).