I have run across that problem using Stamps.com.  I think I just print the label (or envelope) and cross out the street address -- but I'm not sure that's necessary.  It's like if someone gives you both a street address and a PO Box address, because they don't know whether you will ship USPS or UPS, the Post Office knows to use the box number.  (In case you wonder, I make a living with online sales, tax returns are just a hobby.)  

But others will point out that certified mail doesn't prove anything.  You could send an empty envelope to IRS.  It probably slows things down, while it's in the pile that someone signs for once a week.  When I want delivery confirmation, I use Priority Mail or First-Class Package rate.  And I tell my clients not to waste their money on certified, both when sending me stuff and when sending IRS stuff.  It does not get any special handling.  For that, you have to pay lots more for Registered, and the Post Office clerks will always try to talk you out of it because it's a nuisance for them.