What I usually do is that, instead of letting the record process do my mapping for me, I use the NameMapping tool (see screenshot) to manually map those components that I want to work with. This allows me to modify and change things to what I want them to be.
Additionally, after each record, I go back and check my name mapping to make sure that nothing got improperly mapped. If it did, you can click and drag a mapped item between trees and nodes and then delete those extra areas.
Basically, it comes down to doing some due diligence to make sure that your mapping isn't running away on you.