I believe that information is extracted from ABC; if you have ABC installed this information also displays in Pleco.
The only trace I've seen of that is when creating a custom flashcard, but the underdots are removed everywhere else, even when I have ABC as the primary dict.
For example, if creating a custom flashcard from the ABC entry for 过来:
你∼一下。 Nǐ ∼ yị̄xià.
My suggestion is to add dots automatically everywhere. This shouldn't need to change the underlying data, but could be applied at a stage near adding tone color.