If we were talking about filtering out complete records, a Filter transformation would be fine to use here.
However, you want to have certain fields set to NULL under certain conditions.
So all you can do is to use some Expression transformation. In this EXP, you will have to check all those combinations (such as WORK_PHN vs. WORK_PHN_BASE) and find out whether any of these checks fits your input record. If so, you will have to set the phone fields accordingly.
In other words: you feed the EXP with the "raw" input data, and you forward "cleaned-up" phone numbers to the target tables.
Only if none of the checks applies, you can filter out that record to tthe exception table: if there's nothing wrong with the input record, why should you write it to the exception table. So this is the only place (as of my understanding of your description) where you can apply a simple Filter transformation.