I thought about that issue, but then I would need to detect the country a user is coming from before I show them a price. So now I am into geo-ip for basic web visitors, and even then sometimes the price will be wrong.
If I do it at checkout time, I am performing sort of a bait-and-switch with customers, which would leave a sour taste in my mouth.
I thought about the idea of adding a surcharge for EU customers since I need to deal with all of this. I don't know enough about international tax law to know if this is ok.
However, the issue is really that it is taking up time from providing a product. Sure, I could charge more, but unlikely enough to hire someone to deal with the issues. Instead it would more likely negatively affect the number of licenses I sell, which would again lead to me probably not being able to afford to pay someone to deal with it for me.
In the end it comes down to the fact that the EU is making it significantly harder for small companies or individuals to sell digital goods. In the end we are talking about every person who writes an ebook, sells some piece of software or sells digital music having to deal with these issues.
It seems the EU is stacking the deck against small companies and instead favoring larger organizations that can afford full-time accountants. Or favoring large companies that then sell VAT services to the individual.