I like TKL for editing, since it's the layout I've been using for more than 20 years and my fingers know exactly where to go.
I've been testing a layered layout briefly with arrow keys and home & end on the left hand and finding it surprisingly easy to get used to (been thinking of making a new version of my board without the dedicated arrows and edit keys and wanted to test a bit), so I think a 60% with a well-designed or customisable function layer wouldn't slow me down much. Just takes a bit of practice to get used to.
I think they should be in a completely different place to what you're used to so you don't get muscle memory confusion. I had this problem with my Roccat Arvo. It has a numpad which switches to arrows and edit keys, but the edit keys are one row lower than on a TKL and this caused major problems for me. Just couldn't get used to it. I find the layered one better, most likely because it is totally different (different hand, home and end next to the up button, etc), but still kind of intuitive.
I had EXACTLY the same experience with the Roccat Arvo. I had been looking for a TKL keyboard for so long and the Arvo looked to be exactly what I was looking for.
After a while I realized that the slightly moved keys killed me. So I removed the keys I did not use on the numpad, thinking that my touch would help me locate the upper half of the navigation cluster. Nope. It did not work. It was infuriating.
The Arvo has been living in a box with a bunch of other rubber domes since then.
This was one of my last attempts before I discovered mechanical keyboards.
And you are also right about the "slightly off" muscle memory effect. It's better to have keys located in completely different locations, so no muscle memory confusion can happen.
And to get back on topic, yes a 60% keyboard gets in the way sometimes. But it's a compromise. The smaller form factor is such a huge advantage in space saved on the desk, less hand travel while working and portability that in the end it's worth it.
But I would say that it is a question open for debate, and that some people will definitely say that the cons win over the pros.
And finally, I think that there is no completely satisfying 60% board at this time. So when one arrives, more people may change their minds about it.