The way you set up to calculate IBU for your system depends entirely upon how your process operates and your perception of bitterness in your beers. I long ago correlated my IBU target to my perception of bitterness from known standards (Boston Lager, and SN Torpedo). In my process, I needed to target about 5% higher than calculated IBU to get the same perception of bitterness from standard boil addition and dry hopped beers.
When I started experimenting with whirlpool/steep hops, I found that I needed to readjust my target to compensate the additional bitterness I was experiencing. I ended up with establishing the time of whirlpool hopping to match the times that I wanted the hops to steep and adjusting the temperature settings to match the amount of additional bitterness I perceived from the whirlpool addition. For my process, I do not carry over any utilization from the boil, and use whirlpool temperatures around 5F lower than I actually achieve during brewing. This gets me the bitterness I want to achieve based upon my taste buds.
But, this is for my process and not yours. I highly recommend taking a beer you have brewed using whirlpool hops and then comparing the perception of bitterness with a commercial beer that has similar published IBU numbers. Do this a few times and adjust the times/temperatures to get something which seems to work for your process and procedures.
In the end, the IBU numbers can be very misleading as they don't always give you the perception that the number should indicate. Unfortunately, it is also the best number to correlate to bitterness that we have at present.
I know this is not a simple answer to your question, but it is really the only way to figure out for your system how to target the IBU number to get the perception to where you want it to be.