€1,000 plus VAT for a rental comp and PAYE return is outrageous!
More like €200 - €250 inc VAT. The rules are there if you have non PAYE income of less that €3,174 and it had been coded into your PAYE Credits then you can use a Form 12 otherwise it's a Form 11. A form 11 has a late filing fee if not filed on time and an interest charge if not paid on time.
If the income less 75% of the interest and other deductions is positive you have a taxable profit, it's not relevant whether it pays the mortgage or not!