There are several reproduction Arduino boards available. How can I check that the board is wired correctly and that the ATmega chip and the other parts are comparable to the official design?
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.
The only way to verify any given board would be to look at the schematic that goes along with it. If the board is from a sketchy eBay source or something similar you may have to ask the seller, or just take your chances.