I’m having the same problem. I created a custom set in the composite font editor that contains the Thai block plus a few other characters used in Thai (all of the characters in Noto Sans Thai, including the zero-width spaces, etc.), and have tried a variety of composite font settings, to no avail.

In the composite font, the pattern seems to be that U+0E48, 0E49, and 0E4C (diacritical tones) do not display when they are directly above a character, although they display when they appear above another tone. I confirmed that these characters are in the custom set I made, and that they display fine in the same non-composite font.
Interesting sidenote, changing the font of the Kanji and Kana character sets changes how these non-displaying tones are displayed – i.e., the “boxes” become wider or narrower. Not sure whether that is pertinent.

Windows 7, InDesign 2019 with Japanese UI exposed (in English), Adobe World Ready Composer applied. Have tried Tahoma, Noto Sans Thai, & Angsana in the composite font, all with the same results.

Is some additionally required control character needed? Alvis Chen noted that a colleague’s composite font worked.