This difference between the two makes me typo all the time. I'd just modify one of the layouts, but I know a lot of research has been put into the arrangement of keys, so I don't want to change it if it'll make me slower.

Well layouts are usually designed with frequency of the letters in mind. For this type of keyboard it is recomended to put more frequent letters to bottom. And in english the frequency goes E T A O and in russian it goes O E A ( after transliteration).

But I doubt the speed difference will be too large. I would choose one layout and stick to it to get best possible speed from it. I am writing this on czech optimized layout.

Thanks!

Letter positions are based on letter frequency in that given language.

https://github.com/dessalines/thumb-key#thumb-key-letter-positions

Okay, I missed that bottom to top part. Thanks!