Currently Filipino, Indonesian, Malay are not among the languages supported by NACL module.
The US keyboard not providing candidates in these languages is intended behavior.

But there is another issue, which is definitely a bug:
"US keyboard" for these three languages (besides English) have the same label in IME menu;
when the three entries are all present in the list and you try to switch from one to another, the check mark always stays on the first selected menu entry.

Bug fixed in CL 181253476:

1. enable Filipino, Indonesian, Malay in language settings;
2. enable US keyboard for those langauges in input method settings;
3. open input method menu, the three entries all show up as "US keyboard";   
   (this is an issue, need to fix in follow-up CL)
4. select one among the three new entries;
5. open the menu again, the selected entry is checked;
6. select another one among the three new entries;
7. open the menu again, and observe -
   expected: the other selected entry is checked;
   actual: the check stays at the first selected entry.

WAI because we don't ship language model for these languages.