I'm not sure I understand the number of questions being posed here.If the piece has vertical edges then you will be able to cut the outline with any size flat bottom tool in your possession,so it puzzles me that you would choose to use something as small as 3mm.You don't give any details of the machine you are using or the size of the project.If I assume there is no ATC it ought to be quite possible to create the shape in two operations as long as you establish a correct Z datum for the second,corner rounding,operation.
First of all you need to check the tool library to verify that the correct details for the tool are there and that you haven't mixed up radius and diameter.If its all good you might usefully re-select the outline and re-calculate the toolpath.Then run the simulation at the highest resolution your computer can handle to see if the outline will be cut correctly.If this part is correct the machining of the corners shouldn't be too much more work,but could take a very long time if you aren't careful.
It may be theoretically possible to machine the radius around the top edge with all manner of tools but I would expect it to be easier with a ball end tool.I would recommend that you find such an item and enter it's details in the tool library.I would also recommend that you add a new layer to the Vectric file and label it machining boundary or similar and then draw a series of curves and lines about a tool diameter away from the lines denoting the edges of the top corner radius in plan view.The when selecting the area to be machined you can use this outline to constrain the area that will be worked on and it will save a lot of time.You may need to experiment with stepover and range of cutting depths to arrive at a viable outcome and you should run the high resolution simulation as often as necessary.You should be able to arrive at a workable outcome.
You will probably need to post process these two operations as separate files unless you have the luxury of an ATC.Just remember to correct the Z datum after a toolchange or to be certain that the tool length in the tool library is accurate if you would rather not fiddle with the Z datum.Run the first sequence and then the second and it should be as modelled.In fact don't run it until the simulation shows that it will be.