Personally, I think this whole massively increased IBU/20-minute-addition-becomes-a-cube-hop-addition-or-whatever thing is a load of crap based on a few people who have desensitised themselves by brewing massively overhopped beers and come up with some crazy tables on the internet and managed to convince a few people. I will believe it when someone brews identical beers side by side under controlled conditions and has the IBU tested.
Consider the following:
- Isomerisation of alpha acids is related to temperature and drops down to about 10% over a 90 minute boil at 70 degrees [1]
- Even when chilling, you whirlpool and let the wort sit for 10-15 minutes to form a tight trub cone
- If you're doing it right, you remove the hops form the wort when you drain the kettle using some kind of filter or a pickup tube/siphon and only take clear wort
- There will be less convection in a cube of wort than in a boiling kettle which will also reduce isomerisation
Hence the hops aren't really in the wort at high enough temperatures any longer than with chilling. There will likely be some compounds left over and it does take a bit longer to cool down, but a 79% increase in bitterness (31.3 to 56.3 IBU)? Seriously?
If you start doing silly things like adding hops to the hot cube then all bets are off though...
Calculations in any brewing software are only a guide anyway based on a variety of approximations. Your best bet is to brew the beer as is and calibrate yourself against a commercial sample (with a published IBU figure) for reference. Then make any adjustments to your process
if necessary to suit your taste.
[1]
http://ift.confex.com/ift/2004/techprogram/paper_25787.htm