For the inability of foreigners to be recognized as permanent workers or employees without APRC’s, I’m relying on Supreme Court precedent (which is not binding, but I predict they’re going to stick with this rule unless/until the LY changes it).
Feel free to post a link or send me a PM. 
You keep your existing seniority (年資), which means it keeps increasing, when you renew your contract with the same employer (assuming the gap between the end of the old contract and the start of the new contract doesn’t exceed 90 days – see LSA Art. 9). This is also true if your new contract is with another branch of the same company or if the company technically gets replaced with another company but de facto stays the same (also SC precedent – let me know if you want a citation). I think this also answers @crusher’s question.