Hmm, really? In the UK, it's simply an offset to the VAT you pay on the form you fill in each quarter – and I assume you are able to generate the totals from your accounting software. Is it really that hard in The Netherlands?
The zero-rating only applies when a vendor is in a different member state in any case. If you're buying from local suppliers, you will be paying the VAT upfront in any case. It's a bit more convenient to have it knocked off upfront but unless you're on some kind of flat-rate scheme I find it hard to see how it's inconvenient unless filing in the Netherlands is an absolute nightmare.