How do you get a smooth enough finish to the floor to lay vinyl on and not
see the outline of the boarded trench? Lino may be a bit tougher, I guess.

You can lay vinyl on plywood, no problem. Ensure that you get the shuttering
right when laying the concrete to give a nice 18mm step (or however thick
your board is) to lay the plywood into. Also, stuff some insulation above
the pipes and below the plywood to eliminate any weird convection effects.
Leave a couple of mm each side of the trench

Christian.