So you mean to drill 2 holes only can you exactly advice within which holes exist on which tube?
To make it internal as much as it is easily possible, you have to put the
* wire running running from the junction box to the shifters
* RD wire
* junction box
inside the frame.
This means you have to drill out the cable entry hole that is behind the headtube (either side of the frame) and the hole in the chain stay.
This is not rocket science. The main thing is to use common sense. Get a pair of vernier calipers and measure the current hole, unplug and measure a Di2 wire and then look if there is enough room the drill the holes out. Remember, you are measuring diameter, but you only drill the half (radius) out of the hole.
Also how do you know there is enough room to put all the wires and the internal junction box inside the area of the BB shel. If this is not a frame that is compatible DI2 it might be that there is no room..?
This frame probably has a hole on the bottom of the bottom bracket and the hole should have a cover. I don't know how the cover is held in place currently (usually shifter cables hold it in place), but remove it and the junction box probably fits between the frame and BB to the main tube. Thats where i put it without any zip ties and it doesnt make any sound there.
Also with your explanation do you mean that the RD cable will be able to run within the housing exit in the frame on the right chainstay (and therefore also is needed to be drilled) or it will have to run outside with some kind of covering kit?
Internal, yes. Otherwise it is hideous. I dislike all the "di2 compatible" frames that actually have the RD wire running outside.
I had a non Di2 compatible frame myself and had to drill out the RD hole.
Actually, a second way came to my mind when writing this.
As the plugs dont fit through the holes, you could also cut one end of the plug off, insert the wire to the frame and later solder the plug back. These are very small wires, so you need somebody with good soldering skills. I personally dislike it, because the shimano wires are nicely built, but the current first gen DA Di2 requires waterproofing as well, so why not go that route.