The one is using the law, the other is misusing loopholes.
So, there is no intention to deceive, just a simple misunderstanding which leads to very grave problems (as usual when taxes are involved and you are small).
They are and were collecting VAT on their sales. This part is unavoidable regardless.
For the stuff they buy, they're not avoiding VAT. There's no point in avoiding VAT because it doesn't cost a business anything. YOU GET IT BACK FROM THE STATE. The whole point of VAT is that it is a zero-sum game for businesses. But due to their old structure, they're in a situation where they have to pay but can't get back. That's not how VAT is supposed to work.
If you understand the nuance, why are you saying they're dodging taxes? The VAT on the freelancer is related to their business, so it is intended to be recoverable.
So it seems very unlikely that it's an attempt to deceive. If Dmitri isn't involved in the merchandising, it seems that this structure reflects the proper intention of the tax system.
This is a group of passionate people developing a great product and giving it away. I'm not sure any law maker would want to target these guys for tax revenue. I'm not sure the auditors actions represent the spirit of the law.
Splitting an organization in two so the non-profit part can enjoy the benefits the law intends to bestow upon a non-profit is exactly what the government wants you to do.
Separate rules for separate kinds of organizations are a lot easier to make than rules for combined organizations. The latter invites loopholes, but to prevent them the government tends to err on the side of 'anti-loopholes' such as the one the Krita Foundation fell into.
This is not even what the government intends, just an unfortunate side effect.
That is definitely not an attempt to deceive.