First - there's zero issue with water based products under silicone based when we're talking about makeup. All foundation is formulated to behave on top of a surface that is both watery and oily - your skin. The issue would possibly come in to play when you're doing something like applying a layer over of silicone over the skin and possibly creating a surface that water no longer behaves well on (since we usually try to minimize oiliness before applying makeup) - but my one issue with this is also that, generally, silicones used in cosmetic products are generally not water repellent (you can kind of just take my word on this unless you feel like reading a lot of Dow Corning's technical literature - dimethicone is a chained polymer DM-100 and DM-350 are the most common in makeup formulations, water repellant ones like DM-20 and any I've seen larger than DM-1000 aren't typically used on the skin unless you explicitly want a product to be water repellant, like certain sunblocks).

Second, you're never going to find a good or comprehensive list of this because base isn't a technical word or scientific word the way we use it - it's largely determined by manufacturer or some set of rules that whoever decided to apply when making a decision.

I can point out three foundations right away on that list that really questionable being called "water-based" when using the only brand that's been transparent about how they decide on this information's rules (MUFE, water-based for them = only non-volatile silicones in the formula or no silicones at all) - NARS Sheer Glow (which calls itself water-based, silicone enhanced - which is just horrible marketing speak to make their product sound more unique as best I can tell), UD Naked Skin and MAC Face & Body. These formulas contain silicones that are non-volatile and also are not water miscible on their own, they contain other ingredients (usually other types of silicones) that makes the formula play nicely - it's the same strategy used in the products in the silicone-based list. I've personally used both Sheer Glow and MAC Face & Body on top of unquestionably silicone-based primers with zero issue.

I've definitely seen primers and foundation products that don't play nicely together, but I'm not entirely convinced that it's a base-mixing issue majority of the time. I've had silicone-based foundations break down on silicone-based primers. People kind of based this off of paints where you don't see water based formulations that contain silicone and where silicone-based paints typically have some sort of alcohol or solvent carrier rather than water - it's not really an apples to apples comparison.