Yes, all Way- and Markpoints would be available, but you won't have the "connected" picture of the flightplan.
That's why it might be useful (depending on a missions complexity) to work with different flightplans for different stages of the flight.
I for example use a seperate flightplan for my CCIP Mk-82 approaches. For a 45°DB approach it has an IP some 4-5 nm away from the target (heading according to my ingress plans), a Roll-In Point (1.7nm offset target, 90° left/right of my ingress path) and an Aim-Off Point (1.7nm off target, aligned with RIP and target). In the flightplan it will be 1 IP 2 RIP 3 AOP 4 IP. In Flight-Plan Mode your TAD will now draw a nice triangle, which is your planned bomb-pattern. Now add altitudes and appropriate DSMS settings (Z-Diagram) and make some perfect bomb-runs without getting lower than 4.700ft!
:)
Sorry for drifting slightly OT... just thought some might find it interesting...