I've been flying Y and J on MS domestic for the past ten months between Cairo and Luxor, Aswan, Abu Simbel, Sharm el-Sheikh, and Hurghada. I started off in J simply because the fare difference is so minimal, but am now indifferent to which class I'm in. There is no Business class check-in counter for domestic flights. But as mentioned previously, there is almost always no line, unless you walk in to the terminal at the same time as a tour group. There is no priority boarding for J, since all boarding is by bus.
The only difference is the size of seat. If you want a larger seat, pay the $20, otherwise go Y.