The second letter on the residential permits, be it ARC or "Taiwan area residential permit", stands for your sex.
The difference is the issuing authority. If it is A/B, that means your residential permit is issued by the Immigration Department of the Ministry of Interior, and such permits are called "Residential Permit for Taiwan Area of ROC", and this permit may lead you to full ID card later on once you complete the residential requirements. (You need not go through the naturalisation process because you are already deemed to be ROC national, but only without household registration. So once you fullfill the requirements for household registration, you get a full ID card.)
If it is C/D, the residential permit is issued by the Local Police Authority and such permits are called "ARC", and this is issued to most of the foreigners residing in Taiwan. ARC will lead you to APRC once you complete the requirements, but will NOT lead you to full ROC citizenship UNLESS you go through the process of naturalisation. And after naturalisation, your ARC will the changed to the above mentioned "Residential Permit for Taiwan Area of ROC" and C/D would automatically be changed to A/B, and once you complete your residential requirements, you get a full ID.