We have an analogous situation for New Netherland Settlers, except the transition from patronymics to "real" surnames was gradual, and it's often hard to tell what name(s) a person or family was actually using (not to mention wild variations in spelling in the records, due to the mingling of people from the Netherlands, France, England, Scotland, Germany, and other places). A few families used modern-style surnames from the time of first settlement in the first half of the 1600s, while others used patronymics well into the 1700s.
The general rule for New Netherland has been to use a patronymic for the LNAB if it appears (from records and/or from background information about the family and the community) that's what was being at the time of a person's birth. If the person was later identified by a modern-style surname, that goes into the Current Last Name field. Alternate spellings of both patronymics and surnames go into the Other Last Names field. New Netherland women typically didn't use their husbands' names, but if they did, a woman's married name goes into the Current Last Name field, thus increasing the number of Other Last Names.
Yes, the lack of continuity in last names can make it more difficult to keep track of families, but patronyms do make it easier to connect children with their fathers. The New Netherland Settlers project has tried to maintain a modicum of predictability by trying to adopt a consistent LNAB for an entire family (at least there will be one last name for an entire set of siblings), rather than using whatever bizarre spelling shows up in the oldest available record for each child.