I don't think you're quite understanding what people mean when they keep bringing up the weather. You will be fine at the park, but getting home from them is going to be very challenging if you decide to stay at a Skyliner resort during peak hurricane season.
I go in September pretty much every year, usually a Dolphin stay over Labor Day weekend, though last year we went in mid-September for a few days at the Grand before our cruise. I hit Epcot pretty hard on these trips. And it's not an exaggeration to say I see the Skyliner go down every single day. At HS, while inconvenient, it's not that big of a deal because there's only one possible contingency procedure and the bus depot is right next to the Skyliner station. At Epcot however it is always a cluster bleep. There is no set contingency procedure for Skyliner outages at Epcot--sometimes they send guests to Beach Club or BWI to get buses, but sometimes they send guests to the Epcot bus depot for them, which is clear across the park from the Skyliner station. There's no rhyme or reason to it and on the ground communication about what process the magic 8 ball picked that day is very poor. It's not uncommon to pass the IG and see a simple sandwich board telling you to go get a bus in the front of the park, nothing in the app and CMs are often clueless. Vaya con dios if it's still down after fireworks, which I saw one especially miserable Saturday night during F&W. I walked a family to BWI to get buses back to AoA and was very thankful I was staying at BC.
The transportation advantage is totally negated if you're having to take buses anyway. It was irritating enough staying at POFQ in August when I could only take the boat to DS once due to weather. I can't imagine relying on the Skyliner to get to and from actual parks during that time of year.