We know the IRS rules and the lower of rule:

• The amount officially designated  -cash goes to line D
• Your actual housing expenses for the year (mortgage, utilities, repairs, etc.) -For more, see here.
• The Fair Rental Value (FRV) of your home (fully furnished, including utilities) - parsonage goes to line F

The software entry does require the D and F entry as a logic check not to include in wages but carry to SE. You have correctly determined two ways to handle the situation. 

My only caution in using the SE Adj Worksheet is the program is designed to handle the Deason rule from the w2 side. When you go into the SE, you may need to make any required adjustments. Well, you know to double check either way. Great job!