I realize it's a subject that has been discussed before, so I appreciate all of the helpful feedback.
My takeaways:
1) Using a single fermentation phase in a single fermentation vessel for 5 gallon batches should be fine and not result in any off-flavors, from autolysis or otherwise.
2) Secondary fermentation in a second fermentation vessel may be appropriate if adding new fermentables, post-brew day.
3) The off-flavors I have found are most likely due to poor temperature control during primary fermentation.