Most of the transparency effects cause a rasterized output. If you want to have a finer pixelation you will have to change to high resolution transparency flattening.
Why do you want to keep "low"? That is contradictious to you your desire.
Don't flatten the transparency - keep it as live transparency by selecting PDF 5.0 or above.
Transparency Flattener Presets is set to low, and won't switch off low.
It only seems that way. In the same way that PDF presets don't affect the layout, Transparency Flattener presets are not used until output and have no effect on screen display in ID. You choose the correct preset in either the export or print dialog.
That said, as Eugene points out, keeping the transparency live is usually a better option.