The methodology he uses obviously can't work with your system, but I think budding creature designers should bear his points in mind. Once they have worked out a creatures CR, they should then use a method similar to his to see if the final creature is actually reasonable.
I am beginning to suspect that a number of your creatures CRs are inflated because they have a wide array of spell like abilities, but will only get to use a few of them (I'm thinking of Demons and Devils particularly, because I have a lot of experience of using them - some of which have CR's in the MM which are higher than they should be in the MM, too (can anyone say Vrock)).
In this case, the CR's might well be a good representation of ECL (where the full value of all those abilities should be assessed).
I think having a huge range of spell-like abilities is of little value to a monster, if it's only around long enough to use 3 of them.
(And the hit points and fighting ability of most demons ensure sthis will be the case - their high AC & SR is the only thing that makes them last as long as they do - which isn't long at the levels they are often encountered.)
Creatures should pay something for the extra flexibility, yes, but if they have as many abilities as the fiends, I don't think they should pay full value for all those abilities. (As monsters - as PCs they should.)