Per this blog post about Commons' mobile app, it should be possible to allow users that use 2FA to login normally (without BotPassword) by adding a field to the login form to enter the code.
https://addshore.com/2017/05/wikimedia-commons-android-app-pre-hackathon/
https://github.com/commons-app/apps-android-commons/blob/e3ef7002d5d77c1e8cd98c2a72bbc38c8959c276/app/src/main/java/fr/free/nrw/commons/auth/LoginTask.java#L117
https://github.com/commons-app/apps-android-commons/blob/b0e8175003a686789474238dd293aa89d1e925c7/app/src/main/java/fr/free/nrw/commons/mwapi/ApacheHttpClientMediaWikiApi.java#L93
```lang=java
api.action("clientlogin")
.param("rememberMe", "1")
.param("username", username)
.param("password", password)
.param("logintoken", getLoginToken())
.param("logincontinue", "1")
.param("OATHToken", twoFactorCode)
.post()
```