First, my engagements may be different than yours as tax preparation is my primary service.  Your original post indicates that preparing fiduciary returns is an auxiliary service you provide along with your estate administration practice, correct?  I imagine most of your billing is based on billable hours?

I bill tax preparation by the form as it is an easier method for my clients to understand in relation to the value of my service.  It also makes it easier for me to estimate a fee for a prospective client.  And to be honest - I absolutely hate dealing with time keeping.

I determine my base fee to include the actual costs of software, supplies, labor plus an overhead cost componenet (encompassing occupancy, continuing ed, technology, data security, etc) and then a profit component - in my simple mind this means how much do I expect to receive in exchange for the portion of my life I'm giving up to provide this tax return.  That's how I've determined my "Base Fee" just to open a file and prepare the most basic version of that type of return.  Then I assign a fee for the various schedules required to be filed with that form which reflect time at my hourly billing rate.  The client is given the invoice with the base fee assigned to the primary form (1040, 1041, 1065, 1120, etc) and charges for supporting forms detailed below. 

Most years I adjust the base fee to accommodate the increases in my major costs - labor, software overhead.  The whole thing needs to be reviewed some years to make sure I'm still keeping all of my  bases covered.  This is one of those years.