Even if the machine is physically separated, it still needs to be integrated. At the very least, you need a way of telling the machine what is owed and a method for the machine to communicate back that the amount has been payed, and it can't be easily spoofed. Nowadays there is a lot more customer specific integration as well (deals, rebates, signing people up for mailing lists, etc). There are about a dozen different communication standards for POS systems, and some POS systems support more than one, but there are also boatloads of proprietary communications protocols floating around. Presumably you're replacing the POS system with one from the same manufacturer, so the communication protocol is likely to be supported, but that doesn't mean any custom software you have on your system will run as is.
And even if you can hotswap a POS system, they're still expensive. A machine plus software is about $4000 per lane, and that's when you're not a captive market. Even small retailers typically have enough lanes that this is a significant expense. People in this thread are giving prices for Square readers which 1) are not at all sufficient for most businesses and 2) are sold at a loss while Square makes its money on transaction fees and subscription services (the same is true for the rest of the Square clones). It's like comparing a home projector to a movie theater projector.