Do you not see why tax compliant tax payers would be annoyed with you?
To answer your questions, you could have sold the apartment, then you would not have been liable for the stamp duty. You choose not to for whatever reason. You could have come to an arrangment with the bank to repay the negative equity, or probably legitimately could have gone bankrupt where you were working.
You also chose to rent it out and not declare the rent, and you did this because you knew you would be liable for stamp duty.
You are incorrect that due to the 'shortfall' you were not liable for tax on rent, not true, but if you had registered with the PRTB you would have been able to offset mortgage interest against rent.
Nevertheless you are trying to get back on track, and that's good. But I'd be worried about your bank accounts if I were you. And there's the little matter of tenants who claim social welfare rent or tax rent relief without informing the landlord. But you may be lucky and fall thru the net.