Let’s say you naturalize and then get drafted, can your company fire you or do they legally have to wait for you to come back?
lots of companies wont even hire you if you never completed military. Because you could be drafted anytime.
^ this.
Article 44
Citizens who serve in the Military Services are entitled to the following rights：
- During the Active Service or military training period, students shall retain their student status and employees shall retain their original job position and seniority.
https://law.moj.gov.tw/ENG/LawClass/LawAll.aspx?pcode=F0040001
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My sons gave this as an excuse for kicking around and partying before doing their military service- now, they try and blame covid, but it’s starting to wear thin.
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The original says 職工保留底缺年資. A quick search through laws & regulations shows that 職工 is variously translated (not a good sign) as employee or worker. A quick search through court decisions suggests that, tax law aside, businesses can define 職工 however they want in private documents, which leaves the question of who does and doesn’t count as a 職工 for civil law purposes open to debate.
So most people are probably fine, but there are always those employers who claim not to be employers… 
Do they still have to pay you whilst your doing your military service?
My friend told me he only gets $6000 a month from govt
No- they have to/are supposed to hold your job open, but you only get draftee pay from the government.
Legally and actually are 2 very different things. Unless you are actually useful, then they may keep you