The ones I though are this 183 d per year rule and the exemption of a work permit. Though, the latter is not exactly due to the difference between APRCs, but due to the status as a spouse of a Taiwanese, and practically it may often be required.
And iirc, the required documents (financial ones) for naturalization are different too.
Then I think we can say, the APRC itself is the same, but the process for obtaining it is different, and the practical implications of having an APRC while being a foreign spouse are different from those of having an APRC while not being a foreign spouse.
In other words, once you have an APRC, it doesn’t matter how you got it – a “marriage APRC” is just as good as a “non-marriage APRC” – but being married is not just as good (or bad) as not being married. 
Isn’t the 183d rule a difference of the APRC itself? I think the practical implications of having an APRC while being a foreign spouse are not different from those of having an APRC while not being a foreign spouse.
Sorry, I’m confused. What is the legislative basis for treating an APRC holder differently according to how the APRC was obtained?
Iiuc, if you have an APRC and are married, it makes no difference whether you got married first and the APRC later or got the APRC first and married later.
Iiuc, if you get an APRC as a foreign professional and married later, your APRC is exempted from the 183d rule. If you get an APRC as a spouse of a Taiwanese, your APRC is subject of the rule. Isn’t it?
Because they know they are in contradiction with their own laws and rules according work permit/open work permit. (ARC through marriage)
But what’s the basis for that?
Without going into details, there are reasons that people receive an APRC that may not be covered in legislative details. I know right in Taiwan something that happens that isn’t in the books?
And also the treatment. But those situations or probably beyond the situation currently discussed.
It is Article 18 of Act for the Recruitment and Employment of Foreign Professionals.
“Where a foreign professional, after having obtained approval for permanent residence from the National Immigration Agency, Ministry of the Interior, leaves the State for more than five years without re-entering, the National Immigration Agency, Ministry of the Interior, may revoke said person’s permanent residence permit and cancel said person’s Alien Permanent Resident Certificate, and the provisions of Article 33 Paragraph 1 Subparagraph 4 of the Immigration Act do not apply.”
I also found dependant APRCs for spouses and children of foreign professionals can be revoked together when sponsor’s APRC is revoked. So, there are different APRCs.
Articles 15 and 16 of the Act.
It sounds like the deciding factor, then, is whether or not you’re a foreign professional (or dependant of a foreign professional), not simply whether or not you were married when you became a PR. It also seems to say if you become a foreign professional (not having been one when you became a PR), that changes your situation.
I would vote to rewrite the whole system from scatch. 
where is it said? Iirc, an APRC obtained through marriage is subject of the 183d rule, even if you are working as a foreign professional when you get the card. I think how you apply for it decides which APRC you get.
You could read that as meaning if you’re simultaneously a foreign professional and a PR – regardless of how you became a PR – you’re subject to the 5 year rule and not subject to the 183 day (with “special reason” exemptions) rule in the Immigration Act. You could also read it as meaning your foreign professional status at the time of application is what makes the difference.
When they wrote it, they were probably thinking foreigners neatly fall into categories – white professionals over here, brown wives over there, brown laborers nowhere – but of course, many people are both foreign spouses and foreign professionals simultaneously. It reminds me of laws written under the assumption that everyone has one nationality at a time… I suppose we would need to ask for an official clarification to sort it out.
As for dependants, Art. 15
refers to the basis for application, whereas Art. 16
makes reference to employment status but without saying it’s the basis for application.
I think there was a thread that OP reported that he was told by NIA if he got APRC from a marriage based ARC his APRC is subject to the 183d rule, but if he got it from a work based ARC, it is not. OP was a spouse of a Taiwanese, and a foreign professional.