It isn't necessarily isomerization…it is dissolution that is the problem. Isomerized alpha acid have a low solubility in water. If you do partial boils, and then dilute up to 5 gallons, you are limiting the amount of solubilized iso-alpha acids in your final volume which directly relates to IBUs.
The IBU measurement IS the concentration of isomerized alpha acids. I forget what it is specifically but it is something like 1 IBU = 1mg/L of alpha acids. As people well know, there is a cap of IBU around ~100 give or take so 100 mg/L is the maximum solubility of alpha acids.
Here is a fun math experiment for everyone. The golden equation for dilutions is C1V1 = C2V2.
Lets say that you do a 1 gal boil and use 20 oz of hops at 60 minuts. Your max IBU for that 1 gallon is 100 lets say (what ever the cap is). What does your final (theoretical) IBU come out to when you dilute?
V1 = 1 Gallon
C2 = ? IBU
V2 = 5 Gallon
C2 = C1*V1 / V2 = 100*1 / 5 = 20 IBU
One thing that I have thought about for a while is the isomerization. It is well known to happen over temps of 100C so if you are boiling water for an hour, you should be creating more than 100 IBUs worth of isomerized alpha acids. Where do the others go? They have to evaporate off. Anything that doesn't dissolve in the water will be an oil floating at the top of the wort and is most likely being evaporated off. This is probably important to note because it will really impact partial boils. You are most likely converting more than plenty of alpha acids over but you are in turn just boiling them off.