This problem can be largely avoided, for those of us who use a laptop frequently (most of us, I imagine): just leave the laptop layout standard, or lightly modified. I've remapped all of three keys, as a result I can use a stock keyboard with a smallish amount of mental adjustment.
The split key ortho plugged into my monitor, therefore, can be as weird as I want. It's heavily customized and I can do more with it, faster, easier. I do type about 15% faster flat-out with it, but more importantly, I can send λ with little more effort than `l`. But since the laptop has the default layout, I remain "bilingual", two independent muscle memories can be maintained pretty easily if one regularly uses both.
The ortho does have a QWERTY layout for the alphabetic keys, since I don't see the point in changing that, but I don't expect it would make a difference if it didn't.