I have designed another layout called GuiFN
On that one, I'd probably use the pinky for the Fn, not the thumb. (How would I use the thumb for that Fn key without lifting the fingers of my right hand from the home keys?) And, of course, that is the layout (as far as the position of the Fn key goes) that is actually in use by the Poker II keyboard.
It's important to note that GuiFN has not been designed with the Poker 2 in mind. It just happens to be compatible with it, and that's something I noticed well after designing it. I have purchased a Poker 2 one month after designing GuiFN and starting testing it on 3 other 60% boards.
Using the Fn key with the thumb is my design choice. It comes from my experience with SpaceFN, which helped me realize that pressing a Fn key with the thumb while the other fingers were on an inverted T arrow cluster was quite natural and easy to learn. If your pinky is pressing on a key, your other fingers have much less freedom, in particular for the kind of movements that we usually do when we use the arrow cluster.
The main goal of SpaceFN and GuiFN has never been to minimize hand travel. The goal was just to allow a 60% board to be as useable as a TKL. But if you consider hand travel, both SpaceFN and GuiFN end up being more efficient than a TKL or a standard full keyboard!
SpaceFN is the most efficient, as your hands almost don't move from the home position.
GuiFN has been created to answer to the objection of using space as a Fn key while keeping most of the advantages of SpaceFN, and it still manages to be more efficient than a standard keyboard, from the point of view of minimizing hand travel. If optimizing hand travel more comes at the cost of using the pinky, I prefer to keep on using the thumb and I give up on hand travel.
Since the pinky is already being used for Shift and Ctrl, I hadn't perceived that as an issue, although I'm not going to say your concern isn't valid. But if an appreciable portion of the keyboard is being used for shifted Fn-functions, one needs an Fn key for both hands.
With SpaceFN, obviously, you just need one Fn key.
With GuiFN, as you have probably noticed, all the secondary functions have been kept, as much as possible, on the right side. All these can be accessed with the right hand only, with the exception of the F1 to F6 keys and CapsLock.
I understand that you have an interest in designing layouts with the best possible arrangement, in absolute terms, and it's a very interesting process. You can just start with a clean slate and be as creative as you want.
I had to work with more stringent constraints: I start from an existing 60% layout where the number and sizes of the keys are already fixed. I try to leave the main layout as standard as possible, taking into account that many people (including me) already have muscle memory for all the characters-generating keys and most of the modifiers.
When you take this into account, it's already a little miracle to be able to come up with something that works. And that does not leave much freedom for an additional Fn key on the other side of the keyboard.