Supports for air handler block intake
The short answer is Yes it will negatively affect the performance of the unit - lower air flow. The supports block the air from going through the opening - like closing off a portion of it. 

So what does this do - it reduces the air flow (like a clogged filter) and what are the effects of dirty or clogged filters ? 
That is your answer to how you will be impacted and what components will be impacted - BOTH the inside unit and outside unit - they need to work harder run longer.

How bad will the impact be ? Your air filter effectively becomes a 16 inch air filter and loses @ 5 inches times the width of the filter (the square inches of Area). You can ask the Manufacturer - email or call their tech support line and ask for details on your model air handler. 

Aside from that answer - it does not really matter and here is why .. You asked the sales company / installer to fix that air handler mounting and they did not. 

1: How did you pay them - credit card or on credit , cash , check ? 

2: Call them back and have them fix it as you had requested, now is the time to do it - you simply wanted it done right and they did not follow your instructions - case in point would you accept it if they put a different unit in than the one you asked for (that was your instructions too) ?

If you paid with a credit card - if the company ho hums, drags feet or refuses to fix it .. dispute the charges and they will not get paid unless it is fixed.