Ash's contention about boil vigour and isomerisation is partially true and almost exclusively do do with whole flower hops. It is basically a physical thing - in a flower, the soft resins are mostly contained within a structure. If you don't poke and bash it a bit via the vigour of the boil - inside that structure is where they will stay.
If you are using pellets though, they break up completely almost straight away and the iso alpha acids very quickly dissolve. From there on isomerisation is primarily about heat (and pH) - any boil that even remotely resembles an acceptable boil for brewing purposes will do absolutely everything required to mix and isomerise properly. Sure - if you tie them up tight in a hop sock, or perhaps you simply heat your wort to barley a simmer you might notice a difference. But you are talking about a difference you might see between utterly calm and normal... the difference between an acceptable boil on the gentle end of the scale and an acceptable boil on the aggressive end of the scale would be basically non existent.
On the other hand - alpha acids absolutely continue to isomerise in the No Chill cube. I have dozens and dozens of brew's worth of experience to say thats true, and I also have tested the iso alpha acid levels of no-chilled worts to see by how much its true.
In my tests (which could stand a couple of repeats to make them statistically valid) I found that no-chilled worts tended to have an increase in bitterness over chilled worts roughly equivalent to that you would get by boiling all the hop additions for 10-20mins longer than you actually did. So your 60min hops contribute bitterness like they were 70-80min hops and your 5min hops contribute like 15-25 min hops etc etc
That is though specifically for pellet hops added loose in the kettle and assumes you leave behind your trub and hops when you transfer to your NC cube. (Removing the plant matter does not stop this from happening, the acids are already in solution by now). It would not be the same for whole hops, for hops in a hop sock or if you No-Chill in the kettle along with all the hop trub. The bitterness will still increase... but the quantum of that increase is going to be different and I have no suggestions as to how much. And it might not work that way for you - thats just how it worked out in the tests I did.
I also tested for hop pellets added directly to the no-chill cube that never saw the inside of the kettle. Wort into cube, greenery into cube - seal it up and let it cool (moving it about a little every now and again). I found that those "Cube Hops" contributed to bitterness as though they had been in the boil for 25-30mins and the wort had been rapidly cooled. The notion of gentle vs rapid boil is in my experience visible in this situation, because if you put those pellet hops inside a tightish bag (in my case an ankle high stocking/sock) they contribute noticeably less bitterness than if they are loose. If you shake the cube a few times vs just leaving it sit undisturbed after adding the hops... same thing. Noticeable difference in bittering.
The 25-30min figure is for loose pellet hops with the cube moved about a bit over the first few hours. I dont have any sort of a figure for flower hops, hops in a tightish sock or for leaving the cube unmixed - but significantly less bittering for the sock and worth considering with the "still" cube. NFI about flowers, I don't use them.
What I would do to take this stuff into consideration is:
Do not change when you actually put your hops into the boil. Change the time in your software when you are calculating your bitterness and then simply change the quantity of your main bittering addition. So for example
I plan a Pale Ale - it will be a 23L post boil volume @ 1.050 and will have 15g of Chinook (13% AA) as bittering charge @ 60min with 20g of Amarillo (10%AA) at 10mins and another 20g Amarillo at 1min. Pro-mash assumes it will be rapidly chilled and tells me that it will be 38.3 IBUs
BUT - I know that I am going to No-chill the batch and believe that this will increase the bitterness. SO - I tell promash that those hops are all going in the boil 15mins earlier than they really are. 85min, 25min and 16min. Now promash tells me that my new expected bitterness is 50.8 IBU. Now - I adjust the bittering charge down in quantity until the IBUs are back to 38.3. It turns out that that means I am now adding only 8.7g of Chinook. Thats what pro-mash thinks I am going to do.
So now what I actually do is add 8.7g of Chinook as my bittering charge, the Amarillo still gets 20g @ 10mins and 20g at 1 min - and I no-chill.
And that gets me beers that are at the level of bitterness I expect them to be at. It will be different on your system, you will just have to experiment to find out how much you need to "tweak" the boil time you use in your calculations. But if you find you are making over bitter beers and think NC could be the reason - that 15min adjustment is IMO a fairly reasonable place to start your tweaking from.
BTW - I use pro-mash to formulate my recipes and within Pro-mash the Rager IBU calculation formula.
But hops are an art not a science... look at the different formulas, all give different figures for teh same hop additions. No one can agree on how much bitterness you get from a FWH addition, everyone knows you get some bitterness from flameout/whirlpool additions but none of the formulas actually add any IBU's for them. You get different bitterness if you immersion chill vs plate or CF chill and surprise surprise.... you get different bitterness if you No-Chill than you do with chilling. Treat the numbers as a rough guide that will stop you popping an eyeball with a totally over bitter beer and then just go with your tastebuds. They're the only things that really matter anyway.