Well, the stored procedures and UDFs will be ignored already, but for the tables themselves, and especially the columns within the tables, no the DDT won't ignore them. We can ignore the sprocs and udfs by way of an extended property that we put on all StrataFrame items that we can look for. The problem with tables is that there are additional constraints that might change (i.e. foreign key relationships), and that problem grows exponentionally when you start talking about column level changes. For those reasons, we don't plan on accounting for user changes at the table or column level during DDT deployment.
What kind of user customations are your customers doing? There may be a way to enable some level of customization and meet those needs without giving them direct access to the database schema (which is always a bit scary to begin with 
).