So here is some history regarding RV-12 cowl installation.
The photo Tony posted was when the prototype airplane was only about 4 weeks old, based on the date on the photo (it was probably shot at Sun & Fun).
It was still very much a prototype. It had a research and development certificate of airworthiness and it was hauled to S & F in a trailer.
It had a pre-production cowl, and spinner, and cooling radiator duct, and... well, you get the point.
I can not think of what the cause of the spinner missmatch was (it might have even been that the engine position had been shimmed for some flight testing reason, I don't remember).
The airplane as it sits now with 700+ hrs on it, has a spinner that aligns with the top of the cowl.
I am right now in the middle of doing the first condition inspection on the TeenFlight RV-12. It's cowl was installed by teenagers using the before engine is mounted process described in the manual. It's spinner is perfectly aligned with the cowl (I don't have photos, you will have to take my word for it).
Historically, cowls on RV's have been installed after the engine is mounted, using the spinner back plate for reference.
A LOT of builders have still mess it up using this process. Even builders of RV-12's have messed it up while aligning to the spinner (with the help of scribe lines on the cowl).
The manual was written in an attempt to help people get a satisfactory installation without a huge amount of fuss. Someone that is willing to fuss with it, can probably do a bit better, at the cost of more time.
Bottom line...
I believe the current process works if the builder carefully follows the plans.
Installing the engine first also works, but does not assure success (I know of RV-12's built this way and they had engine to air duct interfearances and other problems, so it should not be considered a silver bullet).
The manual is not likely to be rewritten for the reasons already mentioned. The engine first process does not insure that a builder will end up with a good fit, any more than the current process does.
The best over all answer is... There is many different ways to do most building tasks. The manual can only give one. If you think a different way would be better for you, that is of course your choice.