So you DID get a 1099-B? I guess you had two different questions going there and figured you didn't get a 1099-B for the ESPP sales.
"But how about things that I need to do with the broker? Do I need to ask for a modified 1099-B since what's going to the IRS is not accurate? "
NO. Brokers are only responsible for reporting your out of pocket costs.
"My answer was "yes" since the ESPP related income isn't part of my W-2."
Your answer should be "no" if the compensation wasn't on the W-2. Answering "yes" means the compensation ISN'T added to the W-2 because you told TT that the compensation WAS on the W-2.
"And for the 2nd issue on the ESPP topic, is there a way to comment in the actual tax return so that the IRS knows why there is a difference between the 1099-B and the return."
TurboTax does that for you by putting an adjustment in column (g) and a code in column (f).
