You are correct in that E-junkie originated as a digital-commerce, download-fulfillment application first, which later grew from that basis to facilitate shipment of tangible goods as well. However, even then, we were primarily catering to indie creative types (musicians, artists and artisans) and eBayers, who would all be shipping only one or a few items out at a time. Thus, our mantra of simplicity dictated that a basic shipping calculator would meet those needs, using either USPS rate tables or optionally following this basic formula:
((product wt. + package wt.) x (cost per oz.)) + (package cost) + (handling cost)
To disable USPS rate-table calculation, either set all your weights to 0.00, or omit your zipcode as the Shipping Origin from your Seller Admin > Cart Shipping Settings. You may notice here that, for Priority Mail shipments that fit into the standard flat-rate package categories, you can simply leave all the shipping-related settings at 0.00 except for the "package cost", which you would set as equivalent to the Priority Mail flat-rate for that size of package.
We may consider enhancement of our shipping calculation to include other carriers in the future, but for now that's not something we can easily just "bolt on" to the existing E-junkie platform. Implementing a more complicated dynamic lookup (probably interfacing with a third-party API) -- such as would be required for UPS or FedEx (whose rates all vary considerably depending on weight, size and distance, among other factors) -- would require substantial reprogramming of existing code not to mention additional code, so that's something that will probably have to wait until we tackle a ground-up "version 2.0" rewrite of the E-junkie codebase.