That is actually correct. When you trade-in your DEVONthink Pro Office license you’ll rewarded $75 towards the price of DEVONthink 3 and $99 towards DEVONthink Pro 3. Between the standard and Pro editions you’ll later pay just the price difference. So, yes, jumping from V2 to V3 Standard then to V3 Pro is more expensive than going straight through.
As you just recently purchased feel free to contact us for a refund so you can re-purchase directly the upgrade to DEVONthink Pro 3.