The Z axis expansion on pads with and without vias is different which can lead to solder joint cracking on BGA where vias are in some but not all pads. This only occurs on second reflow, so is mostly an issue with BGAs on the first side assembled or after rework in the vicinity. More an issue with thicker PCBs. https://smtnet.com/library/files/upload/transient-solder-separation-bga.pdf
I do use mixed VIPPO on BGAs in some cases but it’s something to be aware of. Where possible, it’s good practice to put a via in every pad including unused ones but this is not always practical.
If your vendor even asks, there’s conductive and non-conductive epoxy fill. For your purposes, you don’t really care. Conductive is mainly a thermal thing and even there it’s only marginally relevant.