I completely agree. My situation is slightly different. I've been using the Windows version for over a year or longer since my primary computers are Windows based.
When I bought my wife a brand new iMac (24 inch, Intel based, etc, etc), she said she would take over putting the receipts in. So, I e-mailed the company to find out if there was anyway I could transfer the license to a Mac version. After several days, I got a response informing me this was not possible and that I would have to purchase NeatWorks (I think it's 4.0, it's close to the newest version). My wife really wanted to do this, so I went ahead and payed the money to buy the NeatWorks software outright, even though I'd already invested a large amount in purchasing the Neatreceipts Software for Windows and the Scanner (in a bundle) when it was first available, so full original retail cost.
After getting the software, it looked nothing like the software I was used to using in Windows, which in a way was good because it was an older version and I had some dislike for the functionality in the older Windows version. Any how, it was expected the UI would be different, so, no big deal, however I couldn't find a simple way to import my data. After some (short) research, I found the utility on their web site to convert data from the Windows version to the Mac version (I don't think this is a 2-way conversion and obviously wouldn't be reliable to keep converting data back and forth anyways). After converting the data and importing it into the Mac version, everything seemed great, thought I was ready to go. Guess again.
Turns out there are as you said, quite a few differences between the Windows version and the Mac version. I actually bought another Mac (Mac Mini) to be able to use the same software as my wife, along with my Windows machines, and so I ended up taking over the receipt scanning again, and the auto-crop and ocr are awful compared to the Windows version. I really hope they fix this soon. Every single receipt I scan in, I have to manually correct something, and I have to go in and crop it manually.
I really expected more after having to purchase a complete new copy of the software, a supposedly NEWER version that functions with lower standards than the older version I was using.