There is no magic - if your employer did not send information under your ID - that information would not be in the IRS computer.
Most likely your accountant knows that - you need to use form 4506T - www.irs.gov/pub/irs-pdf/f4506t.pdf to obtain your tax account transcripts - not form 4506.
On the form 4506T - check the box 8 - Form W-2, Form 1099 series, Form 1098 series, or Form 5498 series transcript. The IRS can provide a transcript that includes data from these information returns.
Also the box 6(a) should be check d for Tax account Transcript.
I suspect that your employer did not issue forms 1099-misc to the IRS - and that was the reason they required to have a business entity.
That is why your income information is not in the IRS system and you never received any notices.
Please be aware that according to the tax law - you are required to report your income regardless if it was reported to the IRS or not.
So technically speaking - the fact of not reporting should not affect your filing requirements or tax liability.
Unfortunately based on very limited information - there is not much we could say.