In VCP's gallery darkroom, we have enlargers mounted directly on the table, this works very nicely, and really opens up the space around the enlarger vs an enlarger on its inch+ thick baseboard. No worries about the easel tipping off the baseboard, and lots of freedom for positioning timers and all the other paraphernalia. That said, my enlarger is on it's baseboard on a standard home-center laminate countertop, but mounting it directly will likely be one of my first changes when I do my "nuke the darkroom and rebuild it" project.
I would consider adding more electrical outlets than you think you need, so that if you add timers, processors, clocks or other power using stuff you won't need to run extension cords, etc.
Concrete wicks water, and produces dust, if it's bare concrete now, you'll want to add some sort of flooring, and depending on what you choose, maybe an additional anti-fatigue mat. I don't know that the grid flooring would be my first choice, unless you have a floor drain (which commercial kitchens usually have). Otherwise cleaning up spills through and around the grid may be very difficult. If you have a floor drain, then all you need is a hose.
Without a drain, my preference would be a flat moisture proof/resistant surface like sheet vinyl.
I would leave the plumbing open for the reasons you've stated, plus it's way easier if you need to make future changes or repairs.