One assumes that a glass neg carrier is being used (else the neg won't be flat anyway) and in my experience the glass surface reflects enough laser light to make mounting a mirror unnecessary during alignment. If you get secondary reflections from further up the optical system (maybe a condenser for example) then just put a piece of masking tape on the top of the neg-carrier glass.
It might simplify starting off with a re-housed enlarger to have the work-table level, the column vertical and the baseboard level - all before checking the head alignment, up and down the column, and finally the lens mount alignment. To check the lens mount, put a microscope slide (or 6x6 slide glass) on the mount, then reflect the laser off that. Some enlargers have no built-in alignment screws, so those are perhaps not the easiest type to start alignment experiments with.
I'm not sure of a reliable way to prove that the elements of a lens are in the correct arrangement regarding the lens-mount - apart from actually trying out the lens of course and/or comparing results to a known good one on the same well-aligned enlarger. One hopes that a Componar-S or Fujinon-EX (and similar standard lenses) would leave the factory in good condition, but a secondhand lens may have had a troubled life, as it were.
How do other people do their routine of checks, and how often?