Here, banks charge up to 0.5% or more to deposit cash (coins), and €0.50 per roll of coins if you need them.
Which country is that?
I know it's not free to deposit coins in many countries, but banknotes are still accepted for free via ATMs.
Could it be the €2 is off the books and won't get taxed, while the €1.99 is handled officially?
It's not possible to avoid issuing a receipt with a POS, because they're interconnected with the tax registry.
With cash payments it's always possible to not issue a receipt and thus not pay VAT (13-24%).
It's kinda risky if they catch you though, because it's compulsory to issue receipts for every type of payment (including BTC).