Placement of evaporator unit on top of furnace (residential)
Your flue is going to be a metal flue screwed together at the joints so it should be fairly easy to remove. I don't know how the access panel is removed but it looks like just a few screws and it possibly can be slid out with the flue still in place. If that's the case then when you route the flue try not to block access to any of the panel screws. I would be more concerned about the routing of the refrigerant lines because those are somewhat permanent. If you have a concern as to how close the flue can to the refrigerant lines, the wall, the drain etc. then post that as a separate question.