Encantona was capable of being mass-produced onboard factory ships even before Operation Moyses, but with no need for that, larger shipyards were responsible for production of fighter- and bombercraft. Main problem of factory ships was their current configuration set to produce mostly missiles, ammunition, spare parts, and plating panels for ORS' modular armor. This configuration was kept after the Exodus, because larger warships [mostly Vitalius frigates] were absolute priority for narrowly escaping Exodus Fleet. Shivan warships were always more dangerous than their smaller craft.
Production of upgraded Encantona was the only possible compromise to fill the gaps in Syndicate's fighter corps and maintain larger warships at full compat readiness all the time, as the Encantona is purely minimalistic and very customizable design. Heretic, despite being modular design, is extremely sophisticated, elite craft. With very limited resources, shivan pursuit, extremely low morale, lots of resources and utility ships lost during the Exodus, broken chain of command and overall situation, Encantona was a necessary compromise.
TLDR: Fleet was a mess, so they were producing mess.
In planned second act, resources will be replenished, all factory ships will be outfitted with new technologies and overally Exodus Fleet will be in much better fighting condition so production of more advanced craft will be fully running. As I mentioned before, main craft of Exodus fleet in The Schism will be ORSified Sabre variant compatible with Syndicate weaponry. Perhaps production of Heretic will be resumed too, but still Exodus Fleet prefer to rely on less-sophisticated and less resource consuming craft. Sabre, as formerly main fighter of EFN fulfill this assumptions.