True, both Taiwanese and Chinese are of the same ethnicity and historically they share the same culture and language. But contrary to what a lot of people believe, Taiwanese and Chinese do not get along with each other, in fact they pretty much hate each other. Similar to North and South Korea, one is capitalist and the other communist. One so called democratic and the other socialist. So philosophically and politically, they are both very different.
Hence I do see why Tibetans and Taiwanese can get along as they both have the same common 'enemy' which is China. Tibetans feel that the Taiwanese can empathise with them in their pursue of autonomy and struggle for independence since Taiwan is also being oppressed by the Chinese. China has always considered Taiwan to be the rogue province. Sounds rather familiar? So it only make sense that the two oppressed little cousins come together to strengthen bonds with each other against big brother China.
For this reason alone, I doubt that there is any hypocrisy in Tibet's action to bond with Taiwan or vice versa.