You can also wack a temporary offloading facility there and lead the civilian transports to unload there to minimize exposure. From there it is only a 20km swim to Chiayi.one use of Penghu is so that tube and shorter ranged rocket artillery can be put to use. due to range limitations, ~100 km is all they'll get. While they can't bombard possible landing beaches for amphibs since there's none around Chiayi across the water from Penghu (it's all wetland), they can cut coastal routes around Chiayi. they can also provide a short ranged drone base and close-in radar station. am I missing anything?
in exchange will be the problem of managing a population of 100k.
Magong port is good for 50,000 tonne class cruise ships, and its on the side facing the mainland. Good place for the RORO ships to come in and unload. The other 1 at longmen is smaller but has cargo handling facilities, so makes for a good secondary logistics hub, for the expendable little ships to do the 20km dash. Having the maritime militia dash a couple hundred tons of good across in hundreds of boats makes it safer for the larger ships.
I would also evacuate the 100k pop back to the mainland and make this place a hornets nest of mobile SAM and SP artillery to pop Taiwanese targets as they come up.