Indeed, a number of EU states are quite aggressive in regards to the use of overseas invoicing companies....they don't accept malta invoice they want to pay the crazy tax in Holland even if the project is 3 months.. same in Germany...
You can still pay all personal taxes in Malta on the income you earn from your projects in the Netherlands or Germany, but this requires a social security (A1, formerly e101) certificate from Malta. And you only get this A1 certificate from Malta if you have a track record of making social security contributions in Malta.
There are rumors of Bulgaria handing out those A1 certificates without proper due diligence. Primarily abused by firms who appoint temporary construction workers across the EU. For the issuing state, every A1 certificate they issue entitles them to tax revenue, even if not much, it's better than nothing. If you want to reduce tax burden, look around for easy opportunities to fetch that A1 certificate from a low tax member state. With A1 certificate, you can work for up to 2 years in another EU country while paying all personal taxes in your "home country".