A couple reasons really that seem to be related...
It can come down to budget and the amount of flow the heads can provide.
There are not as many "big" heads for the 408-427, as compared to the same "big" heads for the 331-347.
For example, if I was to put together a 347, I would seriously look into using the AFR 205cc heads. So, let us stay on the same playing field. The next readily available head from the same company is the 225cc.
There is a 17.5% larger cubic inch volume to fill between a 347 and a 408.
There is 9.7% difference in intake runner volume between the AFR 205cc and AFR 225cc heads.
Or even better, just look at the average cross section numbers between both heads:
AFR 205 - 2.50" (squared)
AFR 225 - 2.74" (squared)
There is only a 9.6% difference between the two heads.
So we are trying to feed more cubes, with potentially, less head flow.
The goals is to fill the added voluve, but 17.5% (between cubes) does not equal 9.6-9.7% (between heads)for the same power potential.
The 408-427 guys really could use more cylinder head, that typically is not out there so readily.
Now, you can port and get speciality heads that the big boys use and have no issues.
But think, porting an AFR 225 head is going to be $3000+ easy.
How many guys are willing to put forth that type of dough?
Few, and far between, which is why you see more smaller cube/high hp, compared to larger cube/high hp. It is typically limited by budget, but relates to engine flow needs as well.
In some applications for higher revving 3.4" guys, I could see even the AFR 225 heads being utilized with the proper package. So what heads, with the same goals, are going to supply enough flow to the 408+ engines?