I have noticed this mainly while playing as retribution.

Divine toll is recommended regardless of how many targets it will hit around you.
Divine toll can hit up to 5 targets around the paladin meaning it will generate 5 holy power.

I have seen it where Divine toll is recommended as the next spell even though I have 8 targets around me but only 4/5 holy power.
Meaning that 4 holy power will be wasted.

Is there a way to include the AoE aspect of divine toll into its recommendation to alleviate over capping on holy power?

Sure. This is the sort of thing one would test by tinkering with sims and verifying that it's worth holding (it probably is). If you complete sims that show a consistent DPS gain, both the simc maintainers and I would be happy to incorporate those updates.

I could not find a performance increase in my own testing, so I have no planned changes for this at this time.