Boat trips

I heard today that the boat trip to Penghu entails an entry and exit stamp in one’s passport, i.e. it counts as leaving and exiting Taiwan. This surprised me, since, as far as I understand, Penghu is just another part of the ROC.
Can anybody who has sailed to Penghu or any of the other small islands that belong to Taiwan fill me in on any entry and exit formalites that may apply.
Also, has anybody recently taken the boat from Gaoxiong that goes out into international waters? Sounds like it may be defunct, as the web address and telephone number don’t connect.
Cheers!