You can seriously use any jacks and wiring you want. ANY.... 2 wire telephone, 4 wire telephone, CAT5, S-Video, RCA, whatever you want. It's just a physical connection for the wires.
The most interesting I've seen was on the Roland forums where someone made a custom rack, then internal custom wiring done using CAT5 from the triggers to a common DSUB connector at the drum set. Then a DSUB type wire from the drum kit to the module. Then a custom wiring loom from the DSUB into whatever jacks are on the module (stereo 6.35mm jacks as it was a Roland module in this particular case). But since you're building your own module you could just as easily use a DSUB right on the MegaDrum if you were so inclined.
So as far as wiring and jacks you can literally use whatever you want. You just need to make sure to wire the MegaDrum end per the schematics. So if you use CAT5 you could theoretically run 7 inputs on that one jack using a common ground then the other individual wires for each input. A 2 line telephone would only support a single input. A 4 wire telephone 3 inputs. And so on and so forth.
Like they say in The Matrix.... FREE YOUR MIND. It's just wires and a physical jack to connect them. Stereo 6.35mm jacks are simply the current "standard" used in the music world these days.
So if you buy a Yamaha cymbal it's going to have a stereo 6.35mm jack. If you use telephone jacks on your MegaDrum you'll then need some custom adapter/cable to connect the two. But if you're building all of your own triggers then you could just use telephone jacks on the triggers and telephone wire to connect the two.
I personally have the 6.35mm stereo jacks on all of my triggers. Then bought a super cheap 20' 16 channel stereo snake off eBay for around $45 shipped to run a single clean line to my equipment rack from the drums into my current Trigger IO which is to be replaced with the MegaDrum.