That is indeed the most significant difference; a paid E-junkie subscription (aka FatFreeCartPro) gives you our Seller Admin screens where you can configure your cart and product settings all in one easy interface, whereas the plain-jane FatFreeCart requires you to configure every detail by hand, for each individual product, right in the HTML source of your Web pages (where anyone can see them, if they want to). There are other things that a Pro subscription can do which the plain, non-Pro cart cannot.
If you need features like location-based sales tax, VAT and shipping calculation, packaging calculator, discounts, inventory management, digital delivery, price verification, affiliate management, managing buyer mailing list, central product management, promotion, accepting Authorize.Net etc. then you would want a subscription to E-junkie's FatFreeCartPro.