Re: .ini settings for ADD KEY to 30Gb table on 96Gb machine?

[Rick James]

VIQA -- When fetching the data, what percent of the rows satisfy the VIQA test?

If most satisfy, then "AND (VIQA & WantedFlags = WantedFlags)" is about as good as you can get. The INDEX(VIQA) is useless for this. (And possibly useless for anything else.)

If very few satisfy, then perhaps your IN approach would be better, but it gets more complicated... I would consider
INDEX(VIQA, PointId)
and use UNION instead of IN.

Another possibility (again for "few satisfy") is to PARTITION on VIQA, and still have INDEX(PointId) (not the compound one)

VIQA is currently 2 bytes; would the IN version take more?

MySQL will almost never use two INDEXes in a single query.