Fn + letters for navigation is much better than dedicated arrow keys, assuming a keyboard with lots of easily accessible thumb keys. Large arm/wrist movements are slow, imprecise, and disruptive.
Maybe for navigation only, but not much if you need combinations for functions like marking a block of text up to a corner of a spreadsheet with 1000+ rows like when editing large data sets. Or when copying formulas over a a column and similar activities.
I've used a 60% for a year and the combination of keys with arrows is very complicated and that lack of dedicated arrows by no means makes the tasks easier. I agree that basic navigation may be more "efficient" because you already have your fingers in the home row, but any other use for arrows gets a little more complicated.
I would like to program some sort of fn+wasd and fn+ijkl as secondary arrow keys, but I am not sure what combination that could be. i am gonna try a script using AHK. I think that could be the best of both, dedicated arrows for the combination functions and secondary arrow keys for the basic navigation. I may try also space fn for that also.
What exactly are you doing? What are the specific key combination that you are using with the arrow keys? Adding shift, alt, and control into the mix is extremely easy. I have to doubt that there is something you can do that would require movement to the arrow keys. When I used Windows I had this all set up to a caps layer using the ahk based pkl (and that's only one way to do it), and it works very well. I would highly recommend you check it out. In particular, I think that control is the most evil key on the keyboard and have totally remapped its functionality.
It may not seem that bad moving your hand to the arrow keys, but after I've forced myself to stop using things that aren't accessible from the home row (I'm working on eliminating the number row right now), I feel that I've benefited a lot from the change. Less use of pinkies. More use of strong fingers. Less movement. Less pain. Greater efficiency.
I honestly never use the arrow keys for anything other than navigation, and I have them mapped to caps + qwerty hjkl. You can even set up a navigation layer to be used when you hold down something like the letter d (I can't really think of a better spot for "fn" ; it requires no movement at all). I assume this could be done with ahk on windows as well. I used to use a program called touchcursor which does this with the space bar (it will act normal unless you hold it and type another key with it).
Even when I'm gaming I don't usually use the arrow keys on my keyboard. Wasd usually suffices, though I do have to use a custom layer lock to get wasd in the right place (if I can't remap movement for the game) since I'm using Colemak. That being said, I like the look of the arrow keys and the numpad, for example, but I never use either.
Also, setting up basic chords on a software level without any sort of custom firmware or special keyboard is totally possible.
An ergonomic board is totally different of a standard rectangular board. The main difference are the thumb + something combinations that just can't be implemented in a regular board.
I think people underestimate what you can do on a normal board. You can, for example, setup the space bar to act as a modifier when held down and pressed with other keys. If you implement a wide mode (shift right hand over one), altgr also becomes more accessible. You can turn caps into a modifier. You can turn letters into modifiers. The sky is the limit. The more people who are interested in this sort of thing, the more support for different operating systems will grow and the more the ease with which these things will be able to be implemented will increase.