Found the issue - WP translations are split across multiple “sub-projects”:
Then under Admin, there is one more sub-project for Network Admin.
I uploaded these other files and got the translated strings up to 78%, which should be higher - around 90-95% - the difference is that many of the WP strings and translations that say WordPress should actually say ClassicPress. So I created separate copies of the .po files to correct for this (just replaced all instances of WordPress with ClassicPress), and then re-uploaded.
For new languages we can download all 4 of those translation files from GlotPress, create copies of the .po files that have WordPress replaced with ClassicPress, and upload all 8 files at once (we need the original 4 also, since some of those strings will still say WordPress). Here are the settings used. The only change from the defaults is to check the box to import strings that do not change when translated, like city names:
Now we are up to 94% translated for Indonesian, and these are steps we can repeat for other new languages. (I still don’t think we should add new languages without a bit more consideration though, we should focus on making the existing ones fully working first.)
Anyway, now Indonesian is ready to follow the steps at Approving and cleaning existing strings on Crowdin.