1. Yes, you can connect this particular version of the mod to your PC directly with a USB cable. You cannot, however, recover from a Gateway brick through this method, as you cannot do low-level eMMC operations through a non-specialized USB reader.
2. The microSD readers you've listed all have boards that are too large to easily fit inside the 3DS's case alongside its mainboard. Additionally, it just so happens that the microSD reader used in this guide is able to read the eMMC chip correctly, where many won't due to limitations on the implementation of the eMMC code used in most of the USB microSD readers. It's a test of luck to find a good microSD reader, so you're going to have to either find the one specified in this guide, or take your chances on finding others that are of the appropriate size and are also compatible. Unfortunately, there is not currently any guide to detail the readers that are compatible, so beyond the posts you'll find in this and similar threads, you're mostly on your own to find one that works.