I noticed this discrepancy too. From what I can figure out playing around with it, it seems like it is equivalent to a hop stand at 94.5C for the amount of time that you enter it. For example, if you put in a hop addition at boil time 0, with a setting of 20 mins in the equipment profile, it will calculate the same IBU's as a whirlpool addition for 20 mins at 94.5C.
I'm obviously not sure how it works 'under the hood' - it seems to me that this is an estimation specifically for the boil additions that carry on into the whirlpool, which keeps them separate from the whirlpool additions. If you used a hop spider and took the boil additions out at the end of the boil, then you could set the equipment profile to 0 and then include your whirlpool additions separately.
For your process (which is similar to mine), I'd suggest that you time how long it takes to get to your target temperature and then adjust the equipment profile to estimate around this. For example, I did a sweet stout today. It took me 5 minutes to get from boiling to 80C at the end of the boil, so I have set my profile for 5 mins. IBUs are really just a guess, anyway, so being out a couple here or there is of little consequence to me in the context of knowing roughly what my system will achieve.
For an IPA, I will (haven't done with BS3 yet) let steep for however long I want my boil additions in - say 10 mins - the add on the ~5 mins to drop my temp to an 80C steep. So my equipment profile will be for 15 mins, with the other hop additions set in the recipe
It seems to me that there is a lot of scope to adjust the equipment in the individual recipe - this is how I'm now recording my individual measures on a brew day, as the "vols" tab still doesn't cut it
Hope that helps