You don't seem to realize that Japan doesn't recognize Taiwan as its own sovereign entity therefore even trying to annexing the island or providing military aid would be seen as an act of war by the PRC.
The Japan-Taiwan Relations Act can only reinforce economic ties not military ones.
I don't think you seem to realize that Japan was a staunch ally and partner of the Republic of China (Taiwan) since the signing of the Treaty of Taipei, it was only during the authoring of Joint Communique between Japan and the PRC that Japan established formal diplomatic relations with the Mainland. With the signing of the 1978 Treaty of Peace and Friendship between Japan and the P.R.C, Japan was forced to abrogate its formal diplomatic relations with Taipei , which was a prerequisite for the TOPF of 1978.
Despite this, the Keidenren (Japanese Business Federation) have long had its influence and operations in Taiwan ever since the signing of the Treaty of Taipei wherein we recognized the formal independence of our Imperial Crown Colony -- Taihoku. I think it is totally feasible to maintain the One China Policy, while also encourage the development of a Japan-Taiwan Relations Act. In fact, the younger brother of Prime Minister Abe, Nobuo Kishi is proposing an new legislative policy within the LDP to establish a Japan - Taiwan Relations Act. This would provide a platform for Japan to provide necessary aid to Taiwan; economic, political and military.