The traditional way of keeping water from getting through a zipper is to use a regular (non-waterproof) zipper and then cover it with a flap. This doesn’t work very well for several reasons:
1) Flaps don’t reliably keep the water out. Flaps can blow open and expose the zipper in high winds. Some of the lighter flaps get crumpled (e.g. DCF flaps) and don’t fully cover the zipper even in gentle conditions. They do block most of the water, but a setup like this isn’t more waterproof than an AquaGuard zipper.
2) Flaps snag in the zipper. It’s very common for flaps to snag in the zipper – especially when you’re running to go pee in the night. The only way to alleviate this is to use a heavier/stiffer flap but then it’s heavier, which brings us to:
3) Flaps add weight. A heavy flap makes it less prone to blowing open and less likely to snag in the zipper, but then it’s heavy. A light flap is obviously lighter but then it doesn’t work very well.
4) It’s clumsy design. Instead of finding a way to improve the zipper to keep water out, a flap adds complexity to the design as a stop-gap measure for the problem. It would be more simple and elegant to simply have a waterproof zipper.
A YKK Aquaguard zipper is a more elegant solution because it makes the zipper fabric waterproof, so the complete zipper is very close to waterproof. The only way water can get in is by leaking through the narrow slit and then through the teeth. That can happen a tiny bit in pounding rains, but in these conditions a flap could easily be worse yet if it’s blowing open. Usually, a bit of leakage is not a problem because any water getting in is happening very slow and it will tend to run down the zipper and drip at the bottom. With my tents, we use Aquaguard zippers for a clean, easier to use, and lighter design and then the zipper panel is steep enough (60 degrees) so that water will virtually never drip off the zipper. Plus we have the zipper is located only over the vestibule, so even if there was a drip it would only land in the vestibule. We think this is a robust solution because the AquaGuard zipper is simple, light, never snags in the zipper, and blocks virtually all the water, and then any leakage does not affect the occupants. So essentially, the drawback of an AquaGaurd zipper can be mitigated with thoughtful design.
In my opinion, an AquaGuard zipper + steep panel + over the vestibule is the best possible design. Sure a 100% waterproof zipper would be better yet, but the only truly waterproof zippers on the market are a lot heavier and hard to use (high friction) like the YKK AquaSeal, so they’re not a viable option for a lightweight tent.
If you have a tent where the zipper is both shallower and over the inner like a traditional mid tent, then using an AquaSeal might be a bit questionable. Some companies with tents like this used to use both an AquaSeal and a flap (e.g. MLD, MSR) but I think they’ve all pretty much done away with the flap because it’s not really adding any performance yet adds weight and tends to snag.
One further note is that Aquaguard zippers don’t do well around a curve because they are higher friction. You get more wear on the zipper so it’s harder to use and can fail sooner. For that reason, some companies opt for regular zippers. For example, you’ll see Hilleberg using regular zippers with flaps on their models that have curved zippers but then when they have a tent with a straight zipper they switch to a nicer Aquaguard zipper. This poor performance around a curve is probably the main reason why regular zippers with flaps remains a popular configuration – that and AquaGuard zippers cost more.