With regards to bolt on, it's simply because you suggested that a well thought out design needs to have the neck flowing into the body (such as neck-through or set-neck), I don't think anyone has described a Fender neck join as 'flowing into the body', yet it will have been thought about an incredible amount from an engineering point of view (as Leo was). So ultimately we have a difference between what you deem to be aesthetically pleasing, and whether something has been thought about.
With regards to the Fodera, everything would have been thought about to the Nth degree. Having owned one previously (although not this model), I found the layout to be ergonomic and intuitive, and can only image that the above is also true.
I actually don't see an issue with it, but I see patterns in groups of things, as opposed to needing an overall uniformed pattern. For example I don't care how the switches are distanced from the EQ, but as long as the EQ is intuitively placed and spaced, then the switches are well placed/spaced in relation to each other etc.
Again, it's simply a difference between what is aesthetically pleasing to you vs whether it's been thought out.....the two aren't mutually exclusive. The headstock shape vs the body shape, that's just the Fodera aesthetic, I don't think it looks weird or unbalanced, but you don't like it. Does that mean 'it hasn't been thought about' or is 'random', no, of course not .
Ultimately, I just think you've been a bit blunt with your point, but it does ultimately boil down to it being totally subjective, same as everything on here.....which is fine, but unfair to accuse any builder of this pedigree of simply 'not thinking about it'.
Si