I’m about to undertake a similar job. I give an estimate based on the description. If I don’t get enough info, I ask for it. My estimate is based on “ideal” circumstance in which the job is as simple as possible. I explain additional options that may drive up cost but increase quality of end product.
I don’t like flat fee work. You almost never win with flat fee work. I let them know what they get for the budget. That’s different than flat fee because it gives you and the client the OPTION to deal with overruns.
When I estimate edit time I include time for changes in that estimate. If they find they want more, that’s one of the overruns they have to grapple with.
In the job I’m about the undertake, it took weeks for the client to get back to me about the room details such as windows, light, etc. It took weeks for the client to give me the list of sections and approximate times.
The client has not yet told me about audience questions although I did tell him the different audio options and the plusses and minuses. The client hasn’t mentioned a word about PowerPoint or other graphic presentations during the seminar although I asked about it and gave him options on shooting vs adding/supplementing in post.
It’s also hard to predict how good public speaker the presenter(s) will be and that impacts editing as you’ve found out. This is why I’d never flat fee a job like this.
I also include the cost of a synced multicam window dub in these types of jobs so the client can see what we/they face in the edit process.
My payment sched on a job like this is: deposit to hold shoot date, payment of shoot and synced window dub on day of shoot, pay for estimated editing time when editing starts (and the amount of time becomes clearer when they see the window dub and decide how much may need to be fixed, cut, graphics added if any).