I mainly use a Noctis for clean up in the Epic Arcs. It takes a bit more prep time before starting each mission but in the long run I’ve found it’s worth it. What I do is move my Noctis with a Shuttle in it to the mission location of the Epic Arc, then take the shuttle back to get my combat ship - bling fit active shield tank AC T3 Loki Cruiser - then accept the mission from the Agent and run it.
Since most of the missions have multiple rooms with a lot of NPC’s in them and to make sure I collect all loot and salvage, I usually only work one room in the mission at a time. Basically I’ll destroy all NPC’s in the room, then dock up and switch to Noctis, clean up the room, dock back up and switch to my combat ship for the next room.
I’ll continue doing that for each room until the mission is completed, then I move the Noctis with a Shuttle in it to the next mission location, shuttle back for my combat ship, accept the next mission and run it the same way as posted above.