"....the total income on Schedule C exceeded the 1099 income. IRS sent a letter to the client looking for the 1099 income - which was already included"

I find that hard to believe; 4 decades of experience and I have never seen that.  Now, if the income reported is LESS than the F 1099's - the IRS will reach out.

OR the F 1099's were MISC v. NEC - especially if the amount was in the wrong box - I can see the IRS questioning. 

And my method isn't 'imprecise.

PTO is based on the same methodology as Lacerte.

Lacerte doesn't have (or need) the function of entering every F 1099 then transferring totals.