Hi. Looks like your accountant is from Tally world. Difficult to make her understand how real ERP work. System is doing the right thing. When user submits information in payment entry system is passing ledger entry.
Either the accountant should read ERPNext manual or you should ignore her.
We have worked with KPMG for their client ERPNext installation. KPMG has tested ERPNext thoroughly before offering it to their clients through us. Grant Thornton has done audit of few of our clients and have not raised any concern.
Go ahead with ERPNext with confidence that it’s one of the rare software that is compliant to accounting standards. FYI. For production use, V12 is the stable one. V13 is still in beta mode.