As far as the long turn and port matching is concerned doing things that make common sense will make improvement,your point that without a flowbench you can't quantify it is valid but doesn't mean its not there.Now when you start messing with the short turn without knowing what your doing or excessively opening the throat below the seat you may start going backwards.Some of the most preeminent engine builders in the country (Jon Kaase off the top of my head)will tell you that quality and not quantity of airflow more significantly correlates to power production and flow benches don't give you that information.
I don't mess with the short turn because I don't know what I'm doing,and I leave the throat sizing to my head guy when he installs the larger valves and only knock off any sharp edges.I also accept that there will be power left on the table,because your exactly right,to get all of it will be trial and error and probably result in a pile of failed experiments.
There are a few things that most can do that will have a very good increase in an engines out put.If you're looking to max it out,hire a professional or be prepared to waste a few head cores as you learn.This could and has happened even when a flow bench is employed by someone who doesn't have experiance .Flow benches,like dyno's are tools that aren't much good unless the people using them know what they're doing.
Your right that is the best feature of the 333's it has the same capabilities as the best of the small port cast iron heads,and is much more available thus lowering price.Also the high price of the large port cast iron heads put them in the unusual situation of with the availability of the aftermarket heads unless you doing a restoration they're not worth spending the money to rebuild them.
The cast iron process itself is more difficult but the iron itself is super cheap. When doing large production runs the cost is spread out and iron comes out cheaper. For small runs aluminum is cheaper. That's how it was explained to me.
Not sure I'm buying that. Think about all of the extra stuff aluminum heads entail, like valve seats, guides, thread inserts and the additional machine operations. Can't see aluminum heads being cheaper than iron in any quantity, or aluminum blocks either. Certainly isn't reflected in the catalog prices? Probably not a big deal; but it always seemed to me like the Eddy 409 heads were sorta over-priced compared to all of their others, even the low-volume ones.