When did that change?
NOTHING has changed. Lacerte, ProSystem FX, UltraTax - all high end tax prep software that I've used in the last four decades, to prepare well over 15,000 tax returns - do NOT require a separate listing. NEITHER does the IRS.
ProSeries (probably) has to assist you in making sure *nothing* gets missed. But it's a tool, that's all.
Your occasional IRS letters were not because a specific Form 1099 was missed in the listing. Most likely they were because of a mismatch of ID numbers & names.
Forms 1099 are supposed to be issued using an individual name & SSN. OR, a business name & a FEIN. If that gets messed up (which I see, regularly) there can be mismatch issues. OR, a client forms an LLC, or incorporates part way thru the year but the F 1099's are issued under the wrong ID number