Yes, I can see that for a non-EU citizen there would be a real problem. However as the EU doesn't allow member states to stamp each others passports, and indeed it is possible for those EU citizens who have National Identity Cards to use them as travel documents I can also see why the ROC government doesn't actually enforce the rules.

They obviously could enforce them on non-EU citizens quite easily, but it would be very difficult to do so for EU citizens unless they kept detailed records of people crossing at the Green Line checkpoint, and since people are (legally speaking) just moving about within the ROC, as the TRNC doesn't exist in international law, the EU free movement regulations come into play. Much better to reserve the right to enforce and keep the moral high ground by not actually doing so.