The total runtime does in fact account for all dwells, overridden or not.
In the case of the Acne 1, the frequency set is defined as:
There are two frequencies with a dwell of 360 seconds as overrides, but the rest will use the default dwell of 180 seconds.
Total time using a dwell multiplier of 1 for this set is (19 frequencies at 180, 2 frequencies at 360) 4140 seconds or 69 minutes. Just happens to be that when you load the frequency set into a program it shows an Estimated Total Run Time of 01:09:00.
To modify this behavior you have two choices.
You can use the dwell multiplier to alter all the frequencies by a multiplier. If you wish for the majority of them to run say at 5 minutes, you could use a dwell multiplier of 1.6667. The two frequencies with a 360 second dwell override will however run at 600 seconds, or 10 minutes rather than the original 6 minutes.
If you do not like this behavior, you will need to create your own custom frequency set, enter in the frequencies, and specify your own default dwell period.
For more details, please check the link: