The side effects of chinese not adopting a phonographic writing system when it could, or having both like japanese does so you don’t need to use such an informal ambiguous layer when actually writing.
That doesn't really solve the problem. Homophones exist, and entering the phonetic representation in some native character set would still require an additional conversion step to disambiguate the homophone. (i.e. in Japanese you can type in hiragana, and many phone IMEs work like that, but you still have to convert that input to kanji; nobody wants to read your long stream of hiragana.) The input methods add value based on how frequently they suggest the correct conversion as the first candidate (based on context).
Imagine typing English by speaking. You can say "flower", but that might get written out as "flour". Some intelligence has to be implemented that picks the right one based on context, or give you the ability to correct it. That is where the complexity in east asian input methods come from.
(Yes, as English-speaking computer users we are very lucky. The exact sort of symbols that readers of English expect map 1:1 to our keyboards. Still kind of a pain on a phone, though!)
I'm not sure I understand your point. Without keeping up with the new memes, IME still let people type them (it's simply not as easy when IME does not auto-suggest the new combination, users can manually select each Chinese character).
Regarding "an informal ambiguous layer", are you implying there is something more fundamental/low-level than the Chinese characters used in communication? If so, what is that?
But native OS IMEs in japan are used frequently, while in China they are not? From what I understand hiragana -> kanji conversions are formalized and thus are easy to add by dumping a dictionary, while in chinese since the phonography is informal you need to do more effort to maintain the dictionary, as everyone ends up typing in whatever they thing they think it would be in pinyin or similar AFAIK, along with all the dialectal variations.
The paper cited for the 68.3% figure http://web.cse.ohio-state.edu/~lin.3021/file/SEC15.pdf says that third-party IMEs are also "very popular" in Japan and Korea, though they do not cite any statistics. (Their statistics for China are from 2014. The paper was published in 2015.)
Chinese orthography is just as standardized as Japanese and hanzi/pinyin dictionaries are not harder to maintain than kanji/hiragana ones. Some people have trouble with sound distinctions in Standard Mandarin that don't exist in their speech and enter incorrect pinyin (e.g. z instead of j or zh), but that can be treated as a typo, the same as phonetic misspellings in other languages.
Support for dialectal variations is essentially nonexistent in mainstream IMEs. People who want to use varieties other than Standard Mandarin would have to use shape-based input (including methods that decompose each character into smaller parts, like Cangjie) or send a voice message. (There are projects to create IMEs for other Sinitic languages, like https://hanhngiox.net/ but almost nobody uses them.)
(Do any Japanese IMEs support non-standard dialects or even other Japonic languages?)
Japanese IMEs are even more complicated than Chinese ones, what are you talking about? (The existence of kana doesn't solve the homophone and homograph problems.)
Imagine typing English by speaking. You can say "flower", but that might get written out as "flour". Some intelligence has to be implemented that picks the right one based on context, or give you the ability to correct it. That is where the complexity in east asian input methods come from.
(Yes, as English-speaking computer users we are very lucky. The exact sort of symbols that readers of English expect map 1:1 to our keyboards. Still kind of a pain on a phone, though!)