The best way to export iphoto library to a certain folder structure

No there isn't. Pretty much the point of iPhoto is that it treats the original file as a "digital negative" and the non-destructive editing feature is based on that. So, iPhoto (and Aperture) never perform any operations on the Original, only on a copy.

It doesn't make multiple versions, tho. There's only one edited version.

What you can do: Export the Edited Versions. Delete the photos from iPhoto. Re-import the edited versions. You'll lose a lot - not least the ability to edit non-destructively - but if that's what you want.

A better solution is to use an app that does what you want - that is, edit the pics directly.

You know that you can store an entire iPhoto Library on a disk formatted Mac OS Extended (Journaled)?

The weight of data (in gigs) doesn't really matter with iPhoto. That's just file storage. If you have a large HD with plenty of free space (30%+ and never less than 10%), it really doesn't matter.

iPhoto used to be rated for 250,000 items in the library, but in the most recent update it has the same format as Aperture, and that is effectively unlimited.

As to how well iPhoto scales: pretty well. I have a 40k plus library that opens in a couple of seconds. I've worked on Libraries in excess of 100k items and while longer to launch (one was almost a minute) it worked fine once open.

You can easily have multiple libraries:

Hold down Option while launching iPhoto, and from the resulting menu select Create Library. Bear in mind that only one can be opened/ searched/ accessed at a time. Again, unless you're getting very large indeed, I would avoid them.

Upgrading to Aperture is simple. Install it. Open the Library. Done.