so is there anything I can do to
mitigate the risk of ruining the flooring in the main room should the
water heater fail after the basement project is complete?

I use these on water heaters, dishwashers, ice makers and washers in
my rental units:

http://www.plumbingsupply.com/floodstopsystems.html

Remember to replace the back-up batteries once a year.

Michael Thomas
Paragon Property Services Inc / Home Inspections
http://paragoninspects.com
847-475-0468