[ue_]

I think the case is different for languages that use the same script, such as a European language learner learning another European language. The learner must learn to switch "modes" and this is reinforced all the time by any kind of reading, because the learner has no choice but to switch modes.

However this mode switching is not reinforced in the case where the script (in this case the Japanese script) is not latin-based.

I think I'm trying to say that native speakers of latin-based languages who are learning latin-based languages have to learn to change their mode of pronunciation, whereas if they were to learn a non-latin-based language they don't (and shouldn't) learn this at all, because in the long run it isn't useful.