Check the quality of not original Arduino boards?
Ultimately, you can't prove that the parts are comparable over the long term without testing them yourself over the long term.  You could certainly construct a very simple test rig and load up the firmata firmware to run each pin through a sanity check when you receive the boards to verify basic functionality.  

When you buy official boards from Arduino, you're buying the trust that they've picked out high quality parts and will offer support if there's a hardware problem.  

There may not be any problem with the variants/clones, but if reliability is the most important concern, official boards are probably the safest bet.