Instead of, or in addition to, changing the number format, you could add some special labels and other cues.
Replace "00:00" with "Start" or something like that.
Once at least one event has been created, place a special label at the end of the last event, like “Ends after 3 h" — which conveys that this is "3 hours long", not "ends at 3 AM / 03:00".
Special labels could also be, or contain, icons symbolizing starting and ending the process, like for example the play/stop symbols (▶️ ⏹) do.
If there's a good phrase or symbol which refers to the actual event that starts the sequence in your particular application then you could include that.
Another idea is that instead of trying to squeeze all information into the left side bar, you could also add a “Start” label and other graphical elements — some kind of visible top edge of the chart — above the chart. To avoid wasting screen space, allow it to scroll up when the chart is scrolled. This would convey that unlike times of day (which extend indefinitely to the past and future), this has a definite beginning.
You could put the duration info and any other interesting summary information below the end of the last event.
An ascii-art sketch of your UI layout with some of these ideas added:
← Example EDIT
Start of sequence |
Start +------------------ <--------- Probably only one of these "Start" labels, not both
| A1 |
:30 | . . . . . . . . . |
| |--- Scrollable area
1:00 |.................. |
| A2 |
1:30 | . . . . . . . . . |
2:00 |.................. |
| A3 |
2:30 | . . . . . . . . . |
3:00 |__________________ <------- Last used time marker might be bolded or something
|[Duration 3 hours] |
3:30 | [blah blah blah ] <------- this footer moves up/down as the last event does
4:30 | |
5:00 | |
[button] [button] [...]